| Next changeset 1:9560828b63f2 (2016-05-27) |
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Commit message:
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty |
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added:
multiqc.xml readme.rst test-data/CollectInsertSizeMetrics.txt test-data/MarkDuplicates_data.txt test-data/bismark_data.txt test-data/collectGcBias_data.txt test-data/cutadapt.txt test-data/fastqc_data.txt test-data/fastqc_data_2.txt test-data/featurecounts_data.txt test-data/log_all.txt test-data/log_bismark.txt test-data/log_cutadapt.txt test-data/log_fastqc.txt test-data/log_fastqc_2.txt test-data/log_featurecounts.txt test-data/log_picard.txt test-data/log_samtools.txt test-data/log_tophat.txt test-data/report_all.html test-data/report_bismark.html test-data/report_cutadapt.html test-data/report_fastqc.html test-data/report_fastqc_2.html test-data/report_featurecounts.html test-data/report_picard.html test-data/report_samtools.html test-data/report_tophat.html test-data/samtools_data.txt test-data/tophat_data.txt tool_dependencies.xml |
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| diff -r 000000000000 -r 8f25feb85166 multiqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc.xml Fri May 27 06:22:43 2016 -0400 |
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| b'@@ -0,0 +1,246 @@\n+<tool id="multiqc" name="multiqc" version="0.6">\n+ <description>aggregate results from bioinformatics analyses across many samples into a single report</description>\n+ <requirements>\n+ <requirement type="package" version="0.6">multiqc</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ mkdir multiqc_WDir;\n+ \n+ #for $i, $repeat in enumerate( $results )\n+\n+ mkdir multiqc_WDir/${repeat.software}_${i};\n+\n+ #if $repeat.software == "fastqc"\n+\n+ #for $k, $file in enumerate ( $repeat.input_file )\n+ ## create a directory for each file because of the unqiue name file parsing\n+ mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};\n+ ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt;\n+ ln -s ${file} multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt;\n+ #end for \n+\n+ #else if $repeat.software == "tophat"\n+\n+ #for $file in $repeat.input_file\n+ ## test if input file name contains align_summary\n+ if [[ \'${file.display_name}\' =~ align_summary$ ]]; then\n+ ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; else\n+ ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; else\n+ ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_align_summary.txt; \n+ ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_align_summary.txt;\n+ fi;\n+ #end for\n+\n+ #else if $repeat.software == "cutadapt"\n+\n+ #for $file in $repeat.input_file\n+ cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt;\n+ ## replace header for old cutadapt release\n+ sed -i \'s/You are running/This is/\' multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; \n+ #end for\n+\n+ #else if $repeat.software == "featurecounts"\n+\n+ #for $file in $repeat.input_file\n+ ## remove spaces and colon to skip multiqc crash\n+ cat ${file} > multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n+ ## remove spaces and colon to skip multiqc crash\n+ sed -i \'s/:/_/g\' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n+ sed -i \'s/ /_/g\' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n+ #end for\n+\n+ #else if $repeat.software == "bismark"\n+\n+ #for $file in $repeat.input_file\n+ ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_SE_report.txt;\n+ ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_SE_report.txt;\n+ #end for\n+\n+ #else\n+\n+ #for $file in $repeat.input_file\n+ cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\';\n+ #if $repeat.software == "picard"\n+\t\t sed -i \'s/picard.sam.markduplicates.MarkDuplicates/picard.sam.MarkDuplicates/\' multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'; \n+\t\t #end if\n+ #end for \n+\n+ #end if\n+ #end for\n+\n+ multiqc multiqc_WDir; \n+ \n+ </command>\n+ <inputs>\n+ <!--param name="inputs" type="data" format="txt" multiple="true" label="Tools logs-outputs" /-->\n+ <repeat name="results" title="Results" min="1">\n+ <param name="software" type="select" label="Software name">\n+ <option value="fastqc">FastQC (RawData file)</option>\n+ <option value='..b'e="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="picard" />\n+ <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_picard.html" compare="sim_size" delta="1000"/>\n+ <output name="text_file" file="log_picard.txt" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="bismark" />\n+ <param name="input_file" value="bismark_data.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>\n+ <output name="text_file" file="log_bismark.txt" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="samtools_stats" />\n+ <param name="input_file" value="samtools_data.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>\n+ <output name="text_file" file="log_samtools.txt" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="fastqc" />\n+ <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="cutadapt" />\n+ <param name="input_file" value="cutadapt.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="tophat" />\n+ <param name="input_file" value="tophat_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="featurecounts" />\n+ <param name="input_file" value="featurecounts_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="picard" />\n+ <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="bismark" />\n+ <param name="input_file" value="bismark_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="samtools_stats" />\n+ <param name="input_file" value="samtools_data.txt" />\n+ </repeat>\n+\n+ <output name="html_file" file="report_all.html" compare="sim_size" delta="3000"/>\n+ <output name="text_file" file="log_all.txt" compare="sim_size" delta="3000"/>\n+ </test>\n+ </tests>\n+\n+\n+ <help>\n+**What it does**\n+\n+MultiQC aggregates results from bioinformatics analyses across many samples into a single report\n+\n+----\n+\n+**Description**\n+\n+MultiQC searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n+\n+----\n+\n+**Inputs**\n+\n+MultiQC takes software outputs summary in order to create a single report. Below a list of compatible Galaxy tools :\n+\n+ - Fastqc\n+ - Cutadapt\n+ - Tophat2\n+ - FeatureCounts\n+ - Samtools stats\n+ - Picard MarkDuplicates metrics\n+ - Picard CollectGTBiasMetrics\n+ - Picard CollectInsertSizeMetrics\n+ - Bismark\n+\n+----\n+\n+**Integrated by:**\n+\n+Cyril Monjeaud and Yvan Le Bras\n+\n+`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility\n+\n+ </help>\n+\n+ <citations>\n+<citation type="bibtex">@proceedings{proceedings,\n+ author = {Phil Ewels, M\xc3\xa5ns Magnusson, Max K\xc3\xa4ller},\n+ title = {Quality control at scale: MultiQC - Intelligent analysis reporting},\n+ journal = {Epigenomics of Common Disease},\n+ year = {2015},\n+ }\n+</citation>\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r 8f25feb85166 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri May 27 06:22:43 2016 -0400 |
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| @@ -0,0 +1,35 @@ +======================== +Galaxy multiqc wrapper +======================== + +Aggregate results from bioinformatics analyses across many samples into a single report + +MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + +============ +Installation +============ + +Requirements: pkg-config + +Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory. + +============ +MultiQC webpage +============ + +Important: For a good view of multiqc webpage, you need to deactivate the sanitize_all_html option in galaxy.ini + + sanitize_all_html = False + +======= +History +======= + + * v0.6: Initial public release + +======= +Citation +======= + +Created by EnginesOn company |
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| diff -r 000000000000 -r 8f25feb85166 test-data/CollectInsertSizeMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CollectInsertSizeMetrics.txt Fri May 27 06:22:43 2016 -0400 |
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| @@ -0,0 +1,737 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/omaha-beach/cloud_26/files/000/dataset_199.dat DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_198.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:33:00 UTC 2016 + +## METRICS CLASS picard.analysis.InsertSizeMetrics +MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP +194 63 100 5331452 271.809759 196.076488 311788 FR 25 47 69 91 127 343 941 1515 2585 16663 + +## HISTOGRAM java.lang.Integer +insert_size All_Reads.fr_count +100 2 +101 117 +102 424 +103 390 +104 376 +105 335 +106 360 +107 343 +108 353 +109 386 +110 349 +111 368 +112 445 +113 459 +114 470 +115 512 +116 478 +117 520 +118 558 +119 599 +120 603 +121 600 +122 696 +123 703 +124 657 +125 747 +126 734 +127 753 +128 820 +129 880 +130 923 +131 931 +132 953 +133 1006 +134 1086 +135 1134 +136 1177 +137 1280 +138 1381 +139 1419 +140 1494 +141 1625 +142 1697 +143 1838 +144 1899 +145 1957 +146 2197 +147 2214 +148 2276 +149 2450 +150 2557 +151 2523 +152 2619 +153 2591 +154 2575 +155 2745 +156 2756 +157 2716 +158 2765 +159 2775 +160 2884 +161 2830 +162 2781 +163 2718 +164 2777 +165 2859 +166 2803 +167 2855 +168 2896 +169 2817 +170 2843 +171 2817 +172 2844 +173 2855 +174 2777 +175 2684 +176 2703 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| diff -r 000000000000 -r 8f25feb85166 test-data/MarkDuplicates_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MarkDuplicates_data.txt Fri May 27 06:22:43 2016 -0400 |
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| @@ -0,0 +1,112 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.sam.markduplicates.MarkDuplicates INPUT=[/omaha-beach/cloud_26/files/000/dataset_114.dat] OUTPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat METRICS_FILE=/omaha-beach/cloud_26/files/000/dataset_196.dat REMOVE_DUPLICATES=false ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:41 UTC 2016 + +## METRICS CLASS picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE +Unknown Library 2900 313405 0 2257 629 0 0.005582 77973949 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 1 +2.0 1.995989 +3.0 2.987982 +4.0 3.975997 +5.0 4.960048 +6.0 5.940152 +7.0 6.916324 +8.0 7.88858 +9.0 8.856937 +10.0 9.821409 +11.0 10.782013 +12.0 11.738763 +13.0 12.691676 +14.0 13.640766 +15.0 14.586049 +16.0 15.52754 +17.0 16.465254 +18.0 17.399207 +19.0 18.329414 +20.0 19.25589 +21.0 20.178649 +22.0 21.097706 +23.0 22.013077 +24.0 22.924776 +25.0 23.832819 +26.0 24.737218 +27.0 25.63799 +28.0 26.535149 +29.0 27.428709 +30.0 28.318684 +31.0 29.20509 +32.0 30.08794 +33.0 30.967248 +34.0 31.84303 +35.0 32.715298 +36.0 33.584068 +37.0 34.449352 +38.0 35.311166 +39.0 36.169523 +40.0 37.024436 +41.0 37.875921 +42.0 38.723989 +43.0 39.568656 +44.0 40.409935 +45.0 41.247839 +46.0 42.082382 +47.0 42.913578 +48.0 43.741439 +49.0 44.565979 +50.0 45.387212 +51.0 46.205151 +52.0 47.019809 +53.0 47.831199 +54.0 48.639334 +55.0 49.444228 +56.0 50.245893 +57.0 51.044342 +58.0 51.839588 +59.0 52.631645 +60.0 53.420524 +61.0 54.206239 +62.0 54.988802 +63.0 55.768226 +64.0 56.544524 +65.0 57.317707 +66.0 58.087789 +67.0 58.854783 +68.0 59.618699 +69.0 60.379551 +70.0 61.137352 +71.0 61.892112 +72.0 62.643845 +73.0 63.392562 +74.0 64.138276 +75.0 64.880999 +76.0 65.620743 +77.0 66.357519 +78.0 67.09134 +79.0 67.822217 +80.0 68.550163 +81.0 69.275188 +82.0 69.997306 +83.0 70.716526 +84.0 71.432862 +85.0 72.146324 +86.0 72.856924 +87.0 73.564674 +88.0 74.269585 +89.0 74.971668 +90.0 75.670935 +91.0 76.367397 +92.0 77.061066 +93.0 77.751952 +94.0 78.440066 +95.0 79.12542 +96.0 79.808025 +97.0 80.487892 +98.0 81.165032 +99.0 81.839456 +100.0 82.511174 + |
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| diff -r 000000000000 -r 8f25feb85166 test-data/bismark_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bismark_data.txt Fri May 27 06:22:43 2016 -0400 |
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| @@ -0,0 +1,39 @@ +Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0) +Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!) +Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet + +Final Alignment report +====================== +Sequences analysed in total: 316390 +Number of alignments with a unique best hit from the different alignments: 220558 +Mapping efficiency: 69.7% +Sequences with no alignments under any condition: 93928 +Sequences did not map uniquely: 1904 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 108352 ((converted) top strand) +CT/GA: 112206 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 5291918 + +Total methylated C's in CpG context: 465068 +Total methylated C's in CHG context: 1358074 +Total methylated C's in CHH context: 3449120 +Total methylated C's in Unknown context: 1499 + +Total unmethylated C's in CpG context: 6399 +Total unmethylated C's in CHG context: 2988 +Total unmethylated C's in CHH context: 10269 +Total unmethylated C's in Unknown context: 454 + +C methylated in CpG context: 98.6% +C methylated in CHG context: 99.8% +C methylated in CHH context: 99.7% +C methylated in Unknown context (CN or CHN): 76.8% |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/collectGcBias_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collectGcBias_data.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,110 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_195.dat SUMMARY_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_193.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/omaha-beach/cloud_26/files/000/dataset_114.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_194.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:30 UTC 2016 + +## METRICS CLASS picard.analysis.GcBiasDetailMetrics +ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP +All Reads 0 0 0 0 0 0 +All Reads 1 0 0 0 0 0 +All Reads 2 0 0 0 0 0 +All Reads 3 10 0 0 0 0 +All Reads 4 7 0 0 0 0 +All Reads 5 6 0 0 0 0 +All Reads 6 4 0 0 0 0 +All Reads 7 9 0 0 0 0 +All Reads 8 22 0 0 0 0 +All Reads 9 15 0 0 0 0 +All Reads 10 20 0 0 0 0 +All Reads 11 18 0 0 0 0 +All Reads 12 101 0 0 0 0 +All Reads 13 118 0 0 0 0 +All Reads 14 137 1 20 0.110575 0.110575 +All Reads 15 243 4 19 0.249362 0.124681 +All Reads 16 366 10 21 0.4139 0.130887 +All Reads 17 468 9 24 0.291322 0.097107 +All Reads 18 689 25 24 0.549664 0.109933 +All Reads 19 1087 40 26 0.557451 0.088141 +All Reads 20 2152 95 25 0.668741 0.068611 +All Reads 21 3279 127 23 0.586731 0.052064 +All Reads 22 5106 178 23 0.528099 0.039583 +All Reads 23 7817 319 23 0.618197 0.034612 +All Reads 24 11933 630 24 0.799774 0.031864 +All Reads 25 17449 759 25 0.658943 0.023918 +All Reads 26 25272 1414 26 0.847591 0.02254 +All Reads 27 34926 1806 25 0.783331 0.018433 +All Reads 28 48489 2889 26 0.90257 0.016792 +All Reads 29 64950 4285 26 0.99942 0.015268 +All Reads 30 84452 5453 26 0.978142 0.013246 +All Reads 31 107535 6476 26 0.912291 0.011337 +All Reads 32 134982 7953 26 0.892548 0.010008 +All Reads 33 165941 9475 26 0.864972 0.008886 +All Reads 34 199087 11437 26 0.870253 0.008137 +All Reads 35 233144 12856 26 0.83533 0.007367 +All Reads 36 266049 14918 26 0.849426 0.006955 +All Reads 37 298999 17019 26 0.862265 0.00661 +All Reads 38 327958 20230 26 0.934446 0.00657 +All Reads 39 350801 22684 26 0.97957 0.006504 +All Reads 40 369841 23670 26 0.969527 0.006302 +All Reads 41 383262 25527 26 1.008975 0.006315 +All Reads 42 392470 26131 25 1.008617 0.006239 +All Reads 43 395234 25603 25 0.981326 0.006133 +All Reads 44 392428 26425 25 1.020074 0.006275 +All Reads 45 386569 25213 25 0.988039 0.006222 +All Reads 46 376763 25980 25 1.044594 0.006481 +All Reads 47 363422 24801 25 1.033795 0.006564 +All Reads 48 348339 24838 25 1.080167 0.006854 +All Reads 49 331960 24992 24 1.140491 0.007214 +All Reads 50 315781 23793 24 1.141405 0.0074 +All Reads 51 297249 22601 24 1.151818 0.007662 +All Reads 52 278159 19653 24 1.070317 0.007635 +All Reads 53 263713 19395 24 1.114127 0.008 +All Reads 54 247317 19047 24 1.166673 0.008453 +All Reads 55 230663 17922 23 1.177023 0.008792 +All Reads 56 215458 16244 23 1.142107 0.008961 +All Reads 57 198515 14904 23 1.137329 0.009316 +All Reads 58 180718 13720 23 1.150083 0.009819 +All Reads 59 165914 11940 23 1.090179 0.009977 +All Reads 60 152561 10775 23 1.069917 0.010307 +All Reads 61 138857 9746 23 1.063249 0.01077 +All Reads 62 125804 9067 22 1.091807 0.011466 +All Reads 63 112222 7148 22 0.964902 0.011413 +All Reads 64 99218 6056 23 0.924638 0.011882 +All Reads 65 85414 5612 24 0.995326 0.013286 +All Reads 66 72999 4286 23 0.88943 0.013586 +All Reads 67 61396 3631 23 0.895907 0.014868 +All Reads 68 52109 3341 22 0.971271 0.016804 +All Reads 69 45121 2735 21 0.918238 0.017558 +All Reads 70 38925 1675 21 0.651873 0.015928 +All Reads 71 32225 1053 22 0.495008 0.015254 +All Reads 72 27537 721 22 0.396639 0.014772 +All Reads 73 23481 483 22 0.311607 0.014179 +All Reads 74 20300 423 22 0.315661 0.015348 +All Reads 75 17785 245 22 0.208684 0.013332 +All Reads 76 15846 236 22 0.225615 0.014686 +All Reads 77 13683 230 22 0.254638 0.01679 +All Reads 78 11733 217 23 0.280174 0.019019 +All Reads 79 10547 188 22 0.270026 0.019694 +All Reads 80 9314 151 22 0.245594 0.019986 +All Reads 81 7659 149 23 0.294707 0.024143 +All Reads 82 5813 56 25 0.145937 0.019502 +All Reads 83 4687 46 23 0.148676 0.021921 +All Reads 84 3505 18 23 0.077797 0.018337 +All Reads 85 2385 8 23 0.050813 0.017965 +All Reads 86 1424 5 21 0.053191 0.023788 +All Reads 87 859 3 20 0.052906 0.030545 +All Reads 88 529 0 0 0 0 +All Reads 89 411 0 0 0 0 +All Reads 90 348 0 0 0 0 +All Reads 91 138 0 0 0 0 +All Reads 92 40 0 0 0 0 +All Reads 93 7 0 0 0 0 +All Reads 94 7 0 0 0 0 +All Reads 95 12 0 0 0 0 +All Reads 96 17 0 0 0 0 +All Reads 97 8 0 0 0 0 +All Reads 98 9 0 0 0 0 +All Reads 99 5 0 0 0 0 +All Reads 100 30 0 0 0 0 + + |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/cutadapt.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt.txt Fri May 27 06:22:43 2016 -0400 |
| b |
| @@ -0,0 +1,129 @@ +You are running cutadapt 1.6 with Python 2.7.3 +Command line parameters: --format=fastq --anywhere=fakadaptater=CACG --error-rate=0.1 --times=1 --overlap=3 --output=/omaha-beach/cloud_26/files/000/dataset_82.dat /omaha-beach/cloud_26/files/000/dataset_33.dat +Maximum error rate: 10.00% + No. of adapters: 1 + Processed reads: 316390 + Processed bases: 31955390 bp (32.0 Mbp) + Trimmed reads: 68795 (21.7%) + Trimmed bases: 3443775 bp (3.4 Mbp) (10.78% of total) + Too short reads: 0 (0.0% of processed reads) + Too long reads: 0 (0.0% of processed reads) + Total time: 5.28 s + Time per read: 0.017 ms + +=== Adapter 'fakadaptater' === + +Sequence: CACG; Length: 4; Trimmed: 68795 times. +2162 times, it overlapped the 5' end of a read +66633 times, it overlapped the 3' end or was within the read + +No. of allowed errors: +0-4 bp: 0 + +Overview of removed sequences (5') +length count expect max.err error counts +3 357 4943.6 0 357 +4 1805 1235.9 0 1805 + + +Overview of removed sequences (3' or within) +length count expect max.err error counts +3 4175 4943.6 0 4175 +4 520 1235.9 0 520 +5 442 1235.9 0 442 +6 522 1235.9 0 522 +7 538 1235.9 0 538 +8 526 1235.9 0 526 +9 482 1235.9 0 482 +10 547 1235.9 0 547 +11 502 1235.9 0 502 +12 539 1235.9 0 539 +13 571 1235.9 0 571 +14 601 1235.9 0 601 +15 537 1235.9 0 537 +16 592 1235.9 0 592 +17 604 1235.9 0 604 +18 617 1235.9 0 617 +19 594 1235.9 0 594 +20 493 1235.9 0 493 +21 558 1235.9 0 558 +22 503 1235.9 0 503 +23 573 1235.9 0 573 +24 609 1235.9 0 609 +25 653 1235.9 0 653 +26 625 1235.9 0 625 +27 541 1235.9 0 541 +28 501 1235.9 0 501 +29 618 1235.9 0 618 +30 539 1235.9 0 539 +31 614 1235.9 0 614 +32 594 1235.9 0 594 +33 627 1235.9 0 627 +34 572 1235.9 0 572 +35 690 1235.9 0 690 +36 615 1235.9 0 615 +37 654 1235.9 0 654 +38 681 1235.9 0 681 +39 530 1235.9 0 530 +40 731 1235.9 0 731 +41 622 1235.9 0 622 +42 611 1235.9 0 611 +43 722 1235.9 0 722 +44 664 1235.9 0 664 +45 659 1235.9 0 659 +46 651 1235.9 0 651 +47 591 1235.9 0 591 +48 642 1235.9 0 642 +49 545 1235.9 0 545 +50 573 1235.9 0 573 +51 591 1235.9 0 591 +52 567 1235.9 0 567 +53 749 1235.9 0 749 +54 647 1235.9 0 647 +55 753 1235.9 0 753 +56 696 1235.9 0 696 +57 780 1235.9 0 780 +58 607 1235.9 0 607 +59 758 1235.9 0 758 +60 643 1235.9 0 643 +61 578 1235.9 0 578 +62 670 1235.9 0 670 +63 652 1235.9 0 652 +64 816 1235.9 0 816 +65 732 1235.9 0 732 +66 640 1235.9 0 640 +67 644 1235.9 0 644 +68 818 1235.9 0 818 +69 658 1235.9 0 658 +70 587 1235.9 0 587 +71 672 1235.9 0 672 +72 588 1235.9 0 588 +73 645 1235.9 0 645 +74 668 1235.9 0 668 +75 725 1235.9 0 725 +76 651 1235.9 0 651 +77 701 1235.9 0 701 +78 662 1235.9 0 662 +79 655 1235.9 0 655 +80 760 1235.9 0 760 +81 746 1235.9 0 746 +82 705 1235.9 0 705 +83 704 1235.9 0 704 +84 726 1235.9 0 726 +85 692 1235.9 0 692 +86 700 1235.9 0 700 +87 758 1235.9 0 758 +88 640 1235.9 0 640 +89 665 1235.9 0 665 +90 848 1235.9 0 848 +91 693 1235.9 0 693 +92 775 1235.9 0 775 +93 1237 1235.9 0 1237 +94 629 1235.9 0 629 +95 574 1235.9 0 574 +96 525 1235.9 0 525 +97 586 1235.9 0 586 +98 696 1235.9 0 696 +99 860 1235.9 0 860 +100 851 1235.9 0 851 + |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/fastqc_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data.txt Fri May 27 06:22:43 2016 -0400 |
| b |
| b'@@ -0,0 +1,2181 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_1\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.91988023102569\t21.0\t21.0\t21.0\t21.0\t21.0\n+2\t20.71684045861661\t21.0\t20.0\t22.0\t19.0\t23.0\n+3\t20.351574954545285\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.531542025544244\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.673566076408722\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.813099918237516\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t27.587864804423386\t28.0\t27.0\t29.0\t26.0\t29.0\n+8\t27.598941941168345\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.07115949658203\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.129873548155864\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t27.009298149330405\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.123565889736383\t28.0\t26.5\t28.0\t26.0\t28.0\n+16-17\t27.086309823818645\t28.0\t26.0\t28.0\t26.0\t28.0\n+18-19\t27.07924614241606\t28.0\t26.0\t28.0\t25.5\t28.0\n+20-21\t27.082520375286073\t28.0\t26.0\t28.0\t26.0\t28.0\n+22-23\t27.054301117420636\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.06350966402712\t28.0\t26.0\t28.0\t25.0\t28.0\n+26-27\t27.082996389756914\t28.0\t26.0\t28.0\t26.0\t28.0\n+28-29\t27.065495857740743\t28.0\t26.0\t28.0\t25.5\t28.0\n+30-31\t27.09608772106672\t28.0\t26.0\t28.0\t26.0\t28.0\n+32-33\t27.087097581099798\t28.0\t26.0\t28.0\t26.0\t28.0\n+34-35\t27.098251253504774\t28.0\t26.5\t28.0\t26.0\t28.0\n+36-37\t27.05184077595959\t28.0\t26.0\t28.0\t25.5\t28.0\n+38-39\t27.06521958267531\t28.0\t26.0\t28.0\t26.0\t28.0\n+40-41\t27.072148859992012\t28.0\t26.0\t28.0\t26.0\t28.0\n+42-43\t27.065725464720796\t28.0\t26.0\t28.0\t25.5\t28.0\n+44-45\t27.07168031241483\t28.0\t26.5\t28.0\t25.5\t28.0\n+46-47\t27.048083061725073\t28.0\t26.0\t28.0\t25.5\t28.0\n+48-49\t27.04642354460909\t28.0\t26.0\t28.0\t25.5\t28.0\n+50-51\t27.062865644448927\t28.0\t26.0\t28.0\t25.5\t28.0\n+52-53\t27.01859629866081\t28.0\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.994157155710866\t27.5\t26.0\t28.0\t25.0\t28.0\n+56-57\t27.110127347871376\t28.0\t27.0\t28.0\t26.0\t28.0\n+58-59\t26.995846540401494\t27.5\t26.0\t28.0\t25.0\t28.0\n+60-61\t27.00461640700544\t27.5\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.981614641085088\t27.5\t26.5\t28.0\t25.5\t28.5\n+64-65\t26.98900313236189\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t27.001189102815392\t28.0\t26.0\t28.0\t25.0\t28.0\n+68-69\t26.917739099268616\t27.5\t26.0\t28.0\t25.0\t28.5\n+70-71\t26.98481793846533\t28.0\t27.0\t28.0\t25.0\t29.0\n+72-73\t26.89518908041471\t27.5\t26.5\t28.0\t25.0\t28.5\n+74-75\t26.93677034448514\t28.0\t27.0\t28.0\t25.0\t29.0\n+76-77\t26.87640237596556\t28.0\t26.5\t28.0\t25.0\t29.0\n+78-79\t26.906094478605482\t28.0\t27.0\t28.0\t25.0\t29.0\n+80-81\t26.80463992772047\t28.0\t26.5\t28.0\t25.0\t29.0\n+82-83\t26.717012197170796\t28.0\t26.5\t28.0\t25.0\t29.0\n+84-85\t26.46960974280285\t27.5\t26.5\t28.0\t25.0\t29.0\n+86-87\t26.442842795754324\t27.5\t26.5\t28.0\t25.0\t29.0\n+88-89\t26.34282375517549\t28.0\t26.0\t28.0\t25.0\t29.0\n+90-91\t26.03493946215965\t28.0\t26.0\t28.0\t24.5\t29.0\n+92-93\t25.833215729758187\t28.0\t26.0\t28.0\t24.0\t29.0\n+94-95\t25.503102494315826\t27.5\t26.0\t28.0\t22.5\t29.0\n+96-97\t24.52807178671565\t27.0\t25.5\t27.5\t21.0\t28.0\n+98-99\t23.202399486277717\t26.0\t24.5\t26.5\t10.0\t27.0\n+100-101\t23.72906749698524\t27.0\t26.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t0.017259946109469126\n+1101\t2\t-0.13408255940416325\n+1101\t3\t-0.11853598095770224\n+1101\t4\t0.015421063929771606\n+1101\t5\t-0.06886052494072459\n+1101\t6\t-0.15241701542762698\n+1101\t7\t-0.029853727500473326\n+1101\t8\t0.04533865186875374\n+1101\t9\t0.07102084333114078\n+1101\t10-11\t0.02726717483210095\n+1101\t12-13\t0.05147474989913192\n+1101\t14-15\t-0.006227419450461014\n+1101\t16-17\t0.051879075943595865\n+1101\t18-19\t0.03525737425918152\n+1101\t20-21\t0.012963832365290529\n+1101\t22-23\t0.02506089814612622\n+1101\t24-25\t0.07843149833360386\n+1101\t26-27\t0.02737786083297422\n+1101\t28-29\t0.005161107012540356\n+1101\t30-31\t-0.08720467946375265\n+1101\t32-33\t-0.017197404032327057\n+1101\t34-35\t0.05763469947927646\n+1101\t36-37\t-0.045600552109540615\n+1101\t38-39\t-0.01952943529413176\n+1101\t40-41\t0.007678874836642535\n+1101\t42-43\t-0.00844'..b'433.5\n+55\t9922.0\n+56\t8785.5\n+57\t7997.0\n+58\t6901.0\n+59\t5796.0\n+60\t4967.0\n+61\t4072.5\n+62\t3639.5\n+63\t3267.0\n+64\t2561.5\n+65\t2002.5\n+66\t1561.5\n+67\t1355.5\n+68\t1222.0\n+69\t1019.0\n+70\t803.0\n+71\t568.5\n+72\t371.5\n+73\t235.0\n+74\t164.5\n+75\t110.5\n+76\t70.5\n+77\t56.0\n+78\t39.5\n+79\t27.0\n+80\t18.0\n+81\t17.0\n+82\t15.5\n+83\t12.5\n+84\t6.5\n+85\t1.5\n+86\t0.0\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.029867574640935753\n+2\t0.0\n+3\t0.003733446830116969\n+4\t0.0\n+5\t3.733446830116969E-4\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.69408840068983\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.5623716290639\t51.950409087115126\n+2\t9.995611185249079\t12.733226849043577\n+3\t3.1947144335386772\t6.104532706343167\n+4\t1.4905270052149588\t3.797510353351082\n+5\t0.8725392208870194\t2.778779513412342\n+6\t0.55360835935223\t2.115694786796508\n+7\t0.38537193434967776\t1.718213983752925\n+8\t0.314619574221819\t1.603152557845755\n+9\t0.2033036957962869\t1.1654319215012086\n+>10\t1.4223398099582591\t15.850860027094066\n+>50\t0.0049931523680946535\t0.18218821374420768\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TTAGTGG\t50\t0.0016122013\t38.00672\t3\n+CCGGGAA\t65\t0.0058204937\t29.246862\t1\n+CTCGCCA\t65\t0.0058204937\t29.246862\t1\n+CCCGCTT\t70\t0.008357804\t27.157803\t1\n+AACAATT\t125\t0.006013185\t19.00336\t2\n+CTGGGAT\t205\t3.3062082E-4\t16.228443\t1\n+AGTTCAA\t195\t0.0044498937\t14.615241\t5\n+GAGTAGT\t125\t0.0014974214\t13.29987\t30-31\n+AAGTTCA\t220\t0.009890434\t12.954418\t4\n+CTGAAAT\t275\t0.003044474\t12.097567\t1\n+CCCAGCT\t405\t3.2130985E-5\t11.734852\t1\n+AGGGTGT\t145\t0.0045575905\t11.465405\t66-67\n+CTGAATT\t335\t0.001024679\t11.349529\t1\n+CTTGAAT\t295\t0.0051441877\t11.277392\t1\n+GAATGTC\t425\t6.555659E-4\t10.058724\t4\n+GGTAGTA\t190\t0.002949709\t9.999902\t52-53\n+CTCTGCC\t390\t0.0036302158\t9.748955\t1\n+CTCCTTT\t535\t5.356131E-4\t8.883393\t1\n+CTTTGCT\t500\t0.0028739348\t8.5547085\t1\n+>>END_MODULE\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/fastqc_data_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data_2.txt Fri May 27 06:22:43 2016 -0400 |
| b |
| b'@@ -0,0 +1,2170 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_2\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.590586487162543\t21.0\t21.0\t21.0\t20.0\t21.0\n+2\t20.458478471078855\t21.0\t19.0\t22.0\t19.0\t22.0\n+3\t20.178608096352797\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.495204387546714\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.59397272343746\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.77560491172265\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t26.651378201897337\t27.0\t26.0\t28.0\t26.0\t28.0\n+8\t27.54968284369178\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.089005372429988\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.058984726469017\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t26.954911162632676\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.066410552214123\t28.0\t26.0\t28.0\t26.0\t28.0\n+16-17\t27.04552938409328\t28.0\t26.0\t28.0\t25.5\t28.0\n+18-19\t27.025118630273028\t28.0\t26.0\t28.0\t25.0\t28.0\n+20-21\t27.019042445557012\t28.0\t26.0\t28.0\t25.0\t28.0\n+22-23\t27.010315513591614\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.03931879529138\t28.0\t26.0\t28.0\t25.5\t28.0\n+26-27\t26.978450544896567\t28.0\t26.0\t28.0\t25.0\t28.0\n+28-29\t27.003714779595967\t28.0\t26.0\t28.0\t25.0\t28.0\n+30-31\t27.025971722873706\t28.0\t26.0\t28.0\t25.0\t28.0\n+32-33\t27.017791740868923\t28.0\t26.0\t28.0\t25.0\t28.0\n+34-35\t27.00628899118533\t28.0\t26.0\t28.0\t25.0\t28.0\n+36-37\t27.00906294218011\t28.0\t26.0\t28.0\t25.0\t28.0\n+38-39\t27.034922661648913\t28.0\t26.0\t28.0\t25.5\t28.0\n+40-41\t27.005346295860726\t28.0\t26.0\t28.0\t25.0\t28.0\n+42-43\t27.000909094303132\t28.0\t26.0\t28.0\t25.0\t28.0\n+44-45\t27.004913216028434\t28.0\t26.0\t28.0\t25.0\t28.0\n+46-47\t26.979999925331065\t28.0\t26.0\t28.0\t25.0\t28.0\n+48-49\t26.941037674211962\t27.5\t26.0\t28.0\t25.0\t28.0\n+50-51\t26.99995146519121\t27.5\t26.0\t28.0\t25.5\t28.0\n+52-53\t26.95084543903468\t27.5\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.97609847339359\t28.0\t26.0\t28.0\t25.0\t28.0\n+56-57\t26.99262270906369\t27.5\t26.0\t28.0\t25.0\t28.0\n+58-59\t26.942271578389317\t27.0\t26.0\t28.0\t25.0\t28.0\n+60-61\t26.88024222603034\t27.0\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.866450873439888\t27.0\t26.0\t28.0\t25.0\t28.0\n+64-65\t26.947610407356386\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t26.975012040366025\t28.0\t26.5\t28.0\t25.0\t28.5\n+68-69\t26.966286975124042\t28.0\t26.5\t28.0\t25.0\t29.0\n+70-71\t26.917634562757375\t28.0\t26.0\t28.0\t25.0\t29.0\n+72-73\t26.885127441207544\t28.0\t26.0\t28.0\t25.0\t29.0\n+74-75\t26.846286527110426\t28.0\t26.5\t28.0\t25.0\t29.0\n+76-77\t26.769134848366058\t28.0\t26.0\t28.0\t25.0\t29.0\n+78-79\t26.709703975000842\t28.0\t26.5\t28.0\t25.0\t29.0\n+80-81\t26.551336760637525\t27.5\t26.0\t28.0\t25.0\t28.5\n+82-83\t26.42626069165836\t27.5\t26.0\t28.0\t25.0\t28.5\n+84-85\t26.309463541024982\t27.5\t26.0\t28.0\t25.0\t29.0\n+86-87\t26.127226534353312\t27.5\t26.0\t28.0\t25.0\t29.0\n+88-89\t25.91885539987082\t27.5\t26.0\t28.0\t24.0\t29.0\n+90-91\t25.674260497519125\t27.0\t26.0\t28.0\t23.5\t29.0\n+92-93\t25.371903572535274\t27.0\t26.0\t28.0\t22.0\t29.0\n+94-95\t24.758753999454918\t27.0\t26.0\t28.0\t20.5\t28.5\n+96-97\t23.84710415196622\t26.5\t25.0\t27.5\t7.0\t28.0\n+98-99\t22.40618968149965\t25.5\t24.0\t26.5\t2.0\t27.0\n+100-101\t23.009550156991438\t27.0\t25.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t-0.1408369887985721\n+1101\t2\t-0.019030947201084558\n+1101\t3\t-0.060059442415557385\n+1101\t4\t0.004085939732711097\n+1101\t5\t-0.018429270835582656\n+1101\t6\t-0.10404524639907464\n+1101\t7\t0.05541229462318498\n+1101\t8\t0.06703529503928962\n+1101\t9\t0.0644374620344621\n+1101\t10-11\t0.06977859906234585\n+1101\t12-13\t0.048103685880093394\n+1101\t14-15\t0.0848396420659725\n+1101\t16-17\t0.030233298636137107\n+1101\t18-19\t0.05253119669850648\n+1101\t20-21\t0.08961672433820667\n+1101\t22-23\t0.014190195653434046\n+1101\t24-25\t-0.013817302849609803\n+1101\t26-27\t0.046003756870838686\n+1101\t28-29\t0.04599618351544166\n+1101\t30-31\t0.04851104267937956\n+1101\t32-33\t0.04656194043190354\n+1101\t34-35\t0.057517795385400916\n+1101\t36-37\t-0.00326392946157128\n+1101\t38-39\t0.0753296536157606\n+1101\t40-41\t0.005995075411309614\n+1101\t42-43\t-0.013913'..b'71.0\n+24\t130.0\n+25\t233.5\n+26\t389.5\n+27\t542.5\n+28\t724.5\n+29\t1063.0\n+30\t1433.0\n+31\t1683.5\n+32\t1996.0\n+33\t2367.5\n+34\t2840.5\n+35\t3318.0\n+36\t3924.5\n+37\t4721.0\n+38\t5510.0\n+39\t6259.0\n+40\t7364.0\n+41\t8736.0\n+42\t9608.5\n+43\t10256.0\n+44\t10928.5\n+45\t11153.5\n+46\t11271.5\n+47\t12042.0\n+48\t12804.5\n+49\t12874.0\n+50\t12482.5\n+51\t11758.0\n+52\t10827.0\n+53\t10433.0\n+54\t10615.0\n+55\t9955.0\n+56\t8760.0\n+57\t7986.5\n+58\t6982.5\n+59\t5802.5\n+60\t4913.5\n+61\t4177.5\n+62\t3751.5\n+63\t3282.0\n+64\t2533.0\n+65\t1954.0\n+66\t1513.0\n+67\t1247.5\n+68\t1102.0\n+69\t957.0\n+70\t777.0\n+71\t535.5\n+72\t361.5\n+73\t253.0\n+74\t157.0\n+75\t99.0\n+76\t60.0\n+77\t46.5\n+78\t37.0\n+79\t21.5\n+80\t13.5\n+81\t16.5\n+82\t19.5\n+83\t14.0\n+84\t6.5\n+85\t3.0\n+86\t0.5\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.11461681768459094\n+2\t0.003733446830116969\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t1.8667234150584845E-4\n+84-85\t0.0\n+86-87\t1.8667234150584845E-4\n+88-89\t0.0014933787320467876\n+90-91\t0.0\n+92-93\t0.0011200340490350907\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.01456044263745618\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.826611251945884\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.66283073871745\t52.122617512935754\n+2\t9.894108596885154\t12.630148461958491\n+3\t3.18062640137576\t6.090258145748586\n+4\t1.5566170090070461\t3.974143548082379\n+5\t0.8538567368205473\t2.7249391002950074\n+6\t0.5533319107768025\t2.119038045746843\n+7\t0.3960736941041749\t1.7696029190496514\n+8\t0.2698969625036296\t1.3781286803040145\n+9\t0.23212846037984958\t1.3334375701059644\n+>10\t1.3969694370078172\t15.730893862039416\n+>50\t0.0035600524217624095\t0.12679215373389083\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TACGAGG\t60\t0.0039460836\t31.665857\t9\n+CCCAGAT\t105\t6.861368E-5\t27.157375\t1\n+AATCAAC\t70\t0.008381328\t27.142164\t5\n+CTTGTAT\t120\t0.004739449\t19.802252\t1\n+TCGCTCA\t130\t0.007549489\t18.268764\t2\n+CCCCACT\t195\t0.0044338168\t14.623201\t1\n+TTCAACA\t295\t0.005166332\t11.270898\t2\n+CTTGAAG\t305\t0.006593838\t10.90747\t1\n+>>END_MODULE\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/featurecounts_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featurecounts_data.txt Fri May 27 06:22:43 2016 -0400 |
| b |
| @@ -0,0 +1,12 @@ +Status 70: TopHat on data 1, data 4, and data 3: accepted_hits 75: TopHat on data 1, data 6, and data 5: accepted_hits 80: TopHat on data 1, data 8, and data 7: accepted_hits 85: TopHat on data 1, data 10, and data 9: accepted_hits 90: TopHat on data 1, data 12, and data 11: accepted_hits 95: TopHat on data 1, data 14, and data 13: accepted_hits +Assigned 321797 445012 394981 437485 388170 453929 +Unassigned_Ambiguity 2333 3424 3121 3692 2782 3554 +Unassigned_MultiMapping 19123 25293 22580 19907 21164 23533 +Unassigned_NoFeatures 111117 165786 129664 146327 132063 160805 +Unassigned_Unmapped 0 0 0 0 0 0 +Unassigned_MappingQuality 0 0 0 0 0 0 +Unassigned_FragmentLength 0 0 0 0 0 0 +Unassigned_Chimera 0 0 0 0 0 0 +Unassigned_Secondary 0 0 0 0 0 0 +Unassigned_Nonjunction 0 0 0 0 0 0 +Unassigned_Duplicate 0 0 0 0 0 0 |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_all.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_all.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,47 @@ +[2016-05-23 10:05:37,586] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 10:05:37,587] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 10:05:37,587] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/107/working +[2016-05-23 10:05:37,587] multiqc [DEBUG ] Template : default +[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 10:05:37,744] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 10:05:37,744] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 10:05:37,744] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpmeCIjG +[2016-05-23 10:05:37,752] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:05:37,754] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:37,757] multiqc.modules.featureCounts.feature_counts [INFO ] Found 6 reports +[2016-05-23 10:05:37,760] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:37,839] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:37,987] multiqc.modules.picard.picard [INFO ] Found 1 dupMetrics reports +[2016-05-23 10:05:37,988] multiqc.modules.picard.picard [INFO ] Found 1 insertSize reports +[2016-05-23 10:05:37,993] multiqc.modules.picard.picard [INFO ] Found 1 GCbias reports +[2016-05-23 10:05:38,017] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 10:05:38,042] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:05:38,079] multiqc.modules.samtools.samtools [INFO ] Found 1 reports +[2016-05-23 10:05:38,104] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:38,111] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports +[2016-05-23 10:05:38,114] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 10:05:38,116] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 10:05:38,118] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:38,121] multiqc.modules.tophat.tophat [INFO ] Found 1 reports +[2016-05-23 10:05:38,146] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:38,170] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:38,196] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports +[2016-05-23 10:05:38,221] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 10:05:38,244] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:05:38,246] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:05:38,313] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports +[2016-05-23 10:05:38,318] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 10:05:38,318] multiqc [INFO ] Data : multiqc_data +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_picard_dups.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_bismark_alignment.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_cutadapt.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_samtools.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_picard_insertSize.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_featureCounts.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_tophat.txt.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' +[2016-05-23 10:05:38,395] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_bismark.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_bismark.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,44 @@ +[2016-05-23 09:52:41,602] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 09:52:41,602] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 09:52:41,602] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/104/working +[2016-05-23 09:52:41,602] multiqc [DEBUG ] Template : default +[2016-05-23 09:52:41,602] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 09:52:41,602] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 09:52:41,603] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 09:52:41,732] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 09:52:41,732] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 09:52:41,732] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpJtZqxl +[2016-05-23 09:52:41,739] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:52:41,743] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,746] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,748] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,756] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,760] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,762] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 09:52:41,765] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:52:41,768] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,771] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,779] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports +[2016-05-23 09:52:41,783] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 09:52:41,786] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 09:52:41,789] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,792] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,794] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,797] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,800] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,803] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 09:52:41,806] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:52:41,809] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,812] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_cpg_meth from general stats table, as no data +[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_chg_meth from general stats table, as no data +[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_chh_meth from general stats table, as no data +[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header total_c from general stats table, as no data +[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header dup_reads_percent from general stats table, as no data +[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header dedup_reads from general stats table, as no data +[2016-05-23 09:52:41,813] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 09:52:41,813] multiqc [INFO ] Data : multiqc_data +[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_bismark_alignment.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' +[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' +[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' +[2016-05-23 09:52:41,907] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_cutadapt.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_cutadapt.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,39 @@ +[2016-05-23 10:04:17,236] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 10:04:17,236] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 10:04:17,236] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/106/working +[2016-05-23 10:04:17,236] multiqc [DEBUG ] Template : default +[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 10:04:17,383] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 10:04:17,383] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 10:04:17,383] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpqOU4l7 +[2016-05-23 10:04:17,390] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:04:17,392] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,394] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,395] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,400] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,403] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,405] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 10:04:17,406] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:04:17,408] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,410] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,413] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,414] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 10:04:17,416] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 10:04:17,418] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,420] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,422] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,424] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,429] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports +[2016-05-23 10:04:17,431] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 10:04:17,433] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 10:04:17,435] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,437] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 10:04:17,437] multiqc.plots.table [DEBUG ] Removing header percent_trimmed from general stats table, as no data +[2016-05-23 10:04:17,438] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 10:04:17,438] multiqc [INFO ] Data : multiqc_data +[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_cutadapt.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' +[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' +[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' +[2016-05-23 10:04:17,517] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_fastqc.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_fastqc.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +[2016-05-23 08:53:43,440] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 08:53:43,440] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 08:53:43,440] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/87/working +[2016-05-23 08:53:43,440] multiqc [DEBUG ] Template : default +[2016-05-23 08:53:43,440] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 08:53:43,441] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 08:53:43,441] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 08:53:43,564] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 08:53:43,564] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 08:53:43,564] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpzTj1_Q +[2016-05-23 08:53:43,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:53:43,573] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,575] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,576] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,589] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,605] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,609] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 08:53:43,614] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:53:43,618] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,623] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,625] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,627] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 08:53:43,629] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 08:53:43,631] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,633] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,637] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,642] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,646] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,651] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 08:53:43,655] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:53:43,657] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:53:43,697] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports +[2016-05-23 08:53:43,702] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 08:53:43,702] multiqc [INFO ] Data : multiqc_data +[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' +[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' +[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' +[2016-05-23 08:53:43,780] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_fastqc_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_fastqc_2.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +[2016-05-23 08:57:23,478] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 08:57:23,478] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 08:57:23,478] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/88/working +[2016-05-23 08:57:23,478] multiqc [DEBUG ] Template : default +[2016-05-23 08:57:23,478] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 08:57:23,479] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 08:57:23,479] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 08:57:23,642] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 08:57:23,642] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 08:57:23,642] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpNoiZ9V +[2016-05-23 08:57:23,648] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:57:23,650] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,652] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,653] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,678] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,706] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,712] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 08:57:23,719] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:57:23,726] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,733] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,735] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,737] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 08:57:23,739] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 08:57:23,741] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,742] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,749] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,756] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,762] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,769] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 08:57:23,776] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:57:23,777] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:57:23,842] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports +[2016-05-23 08:57:23,846] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 08:57:23,846] multiqc [INFO ] Data : multiqc_data +[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' +[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' +[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' +[2016-05-23 08:57:23,919] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_featurecounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_featurecounts.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +[2016-05-23 08:51:46,431] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 08:51:46,431] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 08:51:46,431] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/86/working +[2016-05-23 08:51:46,431] multiqc [DEBUG ] Template : default +[2016-05-23 08:51:46,431] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 08:51:46,431] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 08:51:46,432] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 08:51:46,492] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 08:51:46,492] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 08:51:46,492] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpl8m33T +[2016-05-23 08:51:46,498] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:51:46,500] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,502] multiqc.modules.featureCounts.feature_counts [INFO ] Found 6 reports +[2016-05-23 08:51:46,505] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,508] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,510] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,512] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 08:51:46,513] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:51:46,515] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,516] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,519] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,520] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 08:51:46,522] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 08:51:46,524] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,526] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,527] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,529] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,531] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,532] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 08:51:46,534] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:51:46,535] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,537] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:51:46,538] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 08:51:46,538] multiqc [INFO ] Data : multiqc_data +[2016-05-23 08:51:46,538] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' +[2016-05-23 08:51:46,539] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' +[2016-05-23 08:51:46,539] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_featureCounts.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' +[2016-05-23 08:51:46,610] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_picard.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_picard.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,41 @@ +[2016-05-23 09:33:33,915] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 09:33:33,915] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 09:33:33,916] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/97/working +[2016-05-23 09:33:33,916] multiqc [DEBUG ] Template : default +[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 09:33:34,048] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 09:33:34,049] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 09:33:34,049] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmp4Zyt3V +[2016-05-23 09:33:34,056] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:33:34,057] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,059] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,061] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,069] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,083] multiqc.modules.picard.picard [INFO ] Found 1 dupMetrics reports +[2016-05-23 09:33:34,083] multiqc.modules.picard.picard [INFO ] Found 1 insertSize reports +[2016-05-23 09:33:34,088] multiqc.modules.picard.picard [INFO ] Found 1 GCbias reports +[2016-05-23 09:33:34,091] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 09:33:34,094] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:33:34,097] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,100] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,102] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,104] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 09:33:34,106] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 09:33:34,108] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,110] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,113] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,116] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,118] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,121] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 09:33:34,124] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:33:34,126] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,128] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:33:34,129] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 09:33:34,129] multiqc [INFO ] Data : multiqc_data +[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_picard_dups.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' +[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' +[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_picard_insertSize.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' +[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' +[2016-05-23 09:33:34,206] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_samtools.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_samtools.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +[2016-05-23 09:14:29,851] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 09:14:29,851] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 09:14:29,851] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/89/working +[2016-05-23 09:14:29,851] multiqc [DEBUG ] Template : default +[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 09:14:29,979] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 09:14:29,979] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 09:14:29,979] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpbM5r93 +[2016-05-23 09:14:29,986] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:14:29,988] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:29,989] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:29,991] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,048] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,107] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,120] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 09:14:30,132] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:14:30,157] multiqc.modules.samtools.samtools [INFO ] Found 1 reports +[2016-05-23 09:14:30,170] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,173] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,175] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 09:14:30,177] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 09:14:30,178] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,180] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,193] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,205] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,218] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,230] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 09:14:30,242] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 09:14:30,244] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,246] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 09:14:30,247] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 09:14:30,247] multiqc [INFO ] Data : multiqc_data +[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' +[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_samtools.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' +[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' +[2016-05-23 09:14:30,322] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/log_tophat.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_tophat.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +[2016-05-23 08:46:00,804] multiqc [INFO ] This is MultiQC v0.6 +[2016-05-23 08:46:00,804] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir +[2016-05-23 08:46:00,804] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/85/working +[2016-05-23 08:46:00,804] multiqc [DEBUG ] Template : default +[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml +[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml +[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2016-05-23 08:46:00,928] multiqc [INFO ] Searching 'multiqc_WDir' +[2016-05-23 08:46:00,928] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc +[2016-05-23 08:46:00,928] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpTu_Bvi +[2016-05-23 08:46:00,935] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:46:00,937] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,939] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,940] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,944] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,946] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,948] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2016-05-23 08:46:00,950] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:46:00,951] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,953] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,956] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,957] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2016-05-23 08:46:00,959] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2016-05-23 08:46:00,961] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,964] multiqc.modules.tophat.tophat [INFO ] Found 1 reports +[2016-05-23 08:46:00,966] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,968] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,970] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,971] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) +[2016-05-23 08:46:00,973] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2016-05-23 08:46:00,975] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,977] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2016-05-23 08:46:00,977] multiqc [INFO ] Report : multiqc_report.html +[2016-05-23 08:46:00,978] multiqc [INFO ] Data : multiqc_data +[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' +[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' +[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_tophat.txt.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' +[2016-05-23 08:46:01,051] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_all.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_all.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,4440 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_bismark.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_bismark.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3437 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_cutadapt.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_cutadapt.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3393 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_fastqc.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_fastqc.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3950 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bvhYivhYivhYivhYivhYivhYivhYiwBUiwRQhwRQhwxIh3gEdyBAgQGs2KHs6KXo6KXo5JX06BZI/AJhAAJdAAJdAAJc/AJc+AJc+AJc+AJc8AJ0pBo9XFHyUFnqbFnqaGXemHXG5H2/AHXG5HXG5HXG5HXG4HXG4HXG4HXG4HXG4HXG4HXG4HR0b////FByqhAAAAKp0Uk5TAAAAAAAAAAAAAAESGBcRBgoJnNPQ0rQcWVoLwPtXAqFuv5Mk3NoibP79XQSo+vSbAyzj9+7H4Cl18s7wifFjB7C9nryjBTTpdJFQgOYvfe04Nexot6yXYrKrPeo2heIromkq4ZlrpbFRtW1k/MjUHbuY9ktSw8R673h3M2ETOj08FhiRvLi6aAIJMEtKSkkzBzyxurm6sTkBEj1JSUEeAmq9vL6UHQcWFwlLDobJAAAAAWJLR0SryQFnKAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAAa5JREFUOMut0tdXE0EYBfD9QBRIIgkEDZDQhUBQAgGlBCIlSlGqSlFBVKoiSu8oHQWpIhaUpuD9K50JOXlgJm/cp2/u+Z3dnZ1RFApUqTUa9eVAUk5DQRoWtdaz1gWH6PWhV656CoOeJTTMsw6PAIvR5C4oMoqvEe0B2hhXEet+B8XFy8G1BDdINMtBUrKrIUsKJOD6DSDVyitKS4fZZj4LMjKBm7dcIAvIzhGekGvPgzmfVeS4DRQUCsBmKgKKnaTQnbtASakAjGXlwL37RFQBVFbFCiDJUF0D1BJpHwAPHY/EbdZZ6oEGBzVmcJcqglr+9Y+f0FOgqZmeiaCFnr9gZTibX1qtDSJoJWsb0N6RDaOBHJ0i6CJ69RqV3cCbHtK9lYKeEID9YjuRrkgK6B0/o94+b0ChfhsbBlTegWqQDUMkANeV44DswHAjG84Ap2FkdHSMn2Rz1sg4u8xkMbmb88nE5JSXvP/g48PA9MzsnDzzC4u+DFxY+vhpWZqVz6trfkz4rW9sbknzZfvrRQ52vn3/Ic/P3V+XmPD/vbd/IM/h0R++kYC/x95y8u8/kOgi2/X4mGIAAAAldEVYdGRhdGU6Y3JlYXRlADIwMTYtMDQtMTlUMDk6MjM6NDErMDA6MDCtzsBUAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE2LTA0LTE5VDA5OjIzOjQxKzAwOjAw3JN46AAAAEZ0RVh0c29mdHdhcmUASW1hZ2VNYWdpY2sgNi43LjgtOSAyMDE0LTA1LTEyIFExNiBodHRwOi8vd3d3LmltYWdlbWFnaWNrLm9yZ9yG7QAAAAAYdEVYdFRodW1iOjpEb2N1bWVudDo6UGFnZXMAMaf/uy8AAAAYdEVYdFRodW1iOjpJbWFnZTo6aGVpZ2h0ADE5Mg8AcoUAAAAXdEVYdFRodW1iOjpJbWFnZTo6V2lkdGgAMTky06whCAAAABl0RVh0VGh1bWI6Ok1pbWV0eXBlAGltYWdlL3BuZz+yVk4AAAAXdEVYdFRodW1iOjpNVGltZQAxNDYxMDU3ODIxUvThswAAAA90RVh0VGh1bWI6OlNpemUAMEJClKI+7AAAAFZ0RVh0VGh1bWI6OlVSSQBmaWxlOi8vL21udGxvZy9mYXZpY29ucy8yMDE2LTA0LTE5L2Y2MDUzNWMzMThlMzdlYmRhNzJkZTJlNTJhNWJiNzk5Lmljby5wbme1EtGEAAAAAElFTkSuQmCC">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_fastqc_2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_fastqc_2.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3950 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_featurecounts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_featurecounts.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3409 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwAALiMBeKU/dgAACGNJREFUeNrtnUtsFVUYx3+37xYQ5VHlcbFURHwBPgqICBUkIXHtShcuNCZETdCFRo0LE92yMWiCCxfGLW5MatFaUBCQlJeIighSUeQRBMFSbtvr4ptpT2/vvfPNvTNzprfzS5q0tzPnzJn/fN85833nnAsJCROZVLF/ptNz3F/rgboy67oOZHp7z0TeSKMddU5byqEfuAEQRFtqlMc9BTwNZEuspwrYBmxNp+cM2RDBaesLwJPAUBnlfAJ8GuRFaVgIbCizriZEhHNBXbxPbgWeAZaVWc6eIC+qSnlcqU++yb3AUhjlEkLHqOshYFEARQZxL4bRChAE04C1QHWEdbrUAE8AN1mouyhRCgDQjriCqJkLrLZQrydRC3A38CBE44aMOpYBCyJuq4qoBbgJcQXazj8I6oD1wKSI26oiagFAXMHsCOtrAR610E4VNgS4E2iDcN2QUfYjwHwL7VRhQ4DJiBuqjaCuRsT9NFhopwobAgCsAtIR1HMHsMJSG1XYEmD4xoThhowyVwHzLLVRhS0BXNdQbmCsGFG6upKxJQCE3zkupPy4T+jYFKAFWAnBuiGjrDXALIvtU2FTgHrERTSGUPZUon/hK4kwBMgCg8pjlxNOiOAenJCHgn7Kyw+URRgC9AF7nY'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_picard.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_picard.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3482 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_samtools.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_samtools.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3468 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bvhYivhYivhYivhYivhYivhYivhYiwBUiwRQhwRQhwxIh3gEdyBAgQGs2KHs6KXo6KXo5JX06BZI/AJhAAJdAAJdAAJc/AJc+AJc+AJc+AJc8AJ0pBo9XFHyUFnqbFnqaGXemHXG5H2/AHXG5HXG5HXG5HXG4HXG4HXG4HXG4HXG4HXG4HXG4HR0b////FByqhAAAAKp0Uk5TAAAAAAAAAAAAAAESGBcRBgoJnNPQ0rQcWVoLwPtXAqFuv5Mk3NoibP79XQSo+vSbAyzj9+7H4Cl18s7wifFjB7C9nryjBTTpdJFQgOYvfe04Nexot6yXYrKrPeo2heIromkq4ZlrpbFRtW1k/MjUHbuY9ktSw8R673h3M2ETOj08FhiRvLi6aAIJMEtKSkkzBzyxurm6sTkBEj1JSUEeAmq9vL6UHQcWFwlLDobJAAAAAWJLR0SryQFnKAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAAa5JREFUOMut0tdXE0EYBfD9QBRIIgkEDZDQhUBQAgGlBCIlSlGqSlFBVKoiSu8oHQWpIhaUpuD9K50JOXlgJm/cp2/u+Z3dnZ1RFApUqTUa9eVAUk5DQRoWtdaz1gWH6PWhV656CoOeJTTMsw6PAIvR5C4oMoqvEe0B2hhXEet+B8XFy8G1BDdINMtBUrKrIUsKJOD6DSDVyitKS4fZZj4LMjKBm7dcIAvIzhGekGvPgzmfVeS4DRQUCsBmKgKKnaTQnbtASakAjGXlwL37RFQBVFbFCiDJUF0D1BJpHwAPHY/EbdZZ6oEGBzVmcJcqglr+9Y+f0FOgqZmeiaCFnr9gZTibX1qtDSJoJWsb0N6RDaOBHJ0i6CJ69RqV3cCbHtK9lYKeEID9YjuRrkgK6B0/o94+b0ChfhsbBlTegWqQDUMkANeV44DswHAjG84Ap2FkdHSMn2Rz1sg4u8xkMbmb88nE5JSXvP/g48PA9MzsnDzzC4u+DFxY+vhpWZqVz6trfkz4rW9sbknzZfvrRQ52vn3/Ic/P3V+XmPD/vbd/IM/h0R++kYC/x95y8u8/kOgi2/X4mGIAAAAldEVYdGRhdGU6Y3JlYXRlADIwMTYtMDQtMTlUMDk6MjM6NDErMDA6MDCtzsBUAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE2LTA0LTE5VDA5OjIzOjQxKzAwOjAw3JN46AAAAEZ0RVh0c29mdHdhcmUASW1hZ2VNYWdpY2sgNi43LjgtOSAyMDE0LTA1LTEyIFExNiBodHRwOi8vd3d3LmltYWdlbWFnaWNrLm9yZ9yG7QAAAAAYdEVYdFRodW1iOjpEb2N1bWVudDo6UGFnZXMAMaf/uy8AAAAYdEVYdFRodW1iOjpJbWFnZTo6aGVpZ2h0ADE5Mg8AcoUAAAAXdEVYdFRodW1iOjpJbWFnZTo6V2lkdGgAMTky06whCAAAABl0RVh0VGh1bWI6Ok1pbWV0eXBlAGltYWdlL3BuZz+yVk4AAAAXdEVYdFRodW1iOjpNVGltZQAxNDYxMDU3ODIxUvThswAAAA90RVh0VGh1bWI6OlNpemUAMEJClKI+7AAAAFZ0RVh0VGh1bWI6OlVSSQBmaWxlOi8vL21udGxvZy9mYXZpY29ucy8yMDE2LTA0LTE5L2Y2MDUzNWMzMThlMzdlYmRhNzJkZTJlNTJhNWJiNzk5Lmljby5wbme1EtGEAAAAAElFTkSuQmCC">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/report_tophat.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_tophat.html Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3409 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ \n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- early variable initialisation -->\n+<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n+ \n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n+ </a>\n+ <strong>\n+ <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n+ </strong>\n+ - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n+ available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n+</p>\n+<p>\n+ This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n+ <a href="https://jquery.com/" target="_blank">jQuery</a>,\n+ <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n+ <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n+ and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n+</p>\n+ </div>\n+</div>\n+\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/samtools_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_data.txt Fri May 27 06:22:43 2016 -0400 |
| [ |
| b'@@ -0,0 +1,9736 @@\n+# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /omaha-beach/cloud_26/files/000/dataset_20.dat /omaha-beach/cloud_26/files/000/dataset_114.dat\n+# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n+# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n+CHK\t7742088d\t2cf80e59\t99341a6a\n+# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n+SN\traw total sequences:\t641821\n+SN\tfiltered sequences:\t0\n+SN\tsequences:\t641821\n+SN\tis sorted:\t1\n+SN\t1st fragments:\t320981\n+SN\tlast fragments:\t320840\n+SN\treads mapped:\t641821\n+SN\treads mapped and paired:\t638746\t# paired-end technology bit set + both mates mapped\n+SN\treads unmapped:\t0\n+SN\treads properly paired:\t635626\t# proper-pair bit set\n+SN\treads paired:\t641821\t# paired-end technology bit set\n+SN\treads duplicated:\t0\t# PCR or optical duplicate bit set\n+SN\treads MQ0:\t70\t# mapped and MQ=0\n+SN\treads QC failed:\t0\n+SN\tnon-primary alignments:\t12111\n+SN\ttotal length:\t64823921\t# ignores clipping\n+SN\tbases mapped:\t64823921\t# ignores clipping\n+SN\tbases mapped (cigar):\t64823921\t# more accurate\n+SN\tbases trimmed:\t0\n+SN\tbases duplicated:\t0\n+SN\tmismatches:\t275405\t# from NM fields\n+SN\terror rate:\t4.248509e-03\t# mismatches / bases mapped (cigar)\n+SN\taverage length:\t101\n+SN\tmaximum length:\t101\n+SN\taverage quality:\t26.0\n+SN\tinsert size average:\t719.7\n+SN\tinsert size standard deviation:\t1223.0\n+SN\tinward oriented pairs:\t317512\n+SN\toutward oriented pairs:\t1294\n+SN\tpairs with other orientation:\t30\n+SN\tpairs on different chromosomes:\t0\n+# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n+# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n+FFQ\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t113\t0\t0\t0\t0\t320725\t143\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t4\t320810\t71\t91\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t3\t320877\t25\t75\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t5\t320905\t26\t44\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320816\t67\t86\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t8\t320839\t42\t84\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t6\t320867\t57\t47\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t8\t320845\t59\t64\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t2\t320851\t46\t78\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t4\t320836\t57\t77\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t7\t320849\t46\t67\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t8\t320812\t80\t78\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t9\t320826\t56\t82\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t1\t0\t0\t0\t10\t320774\t77\t107\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t7\t320808\t60\t95\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t1\t0\t0\t0\t12\t320786\t68\t101\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320758\t89\t116\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t9\t320768\t86\t106\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t19\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t12\t320795\t77\t91\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t20\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t11\t320739\t99\t110\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t16\t320681\t115\t143\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t22\t0\t0\t0\t0\t'..b'92-892]\t892\t9\n+COV\t[893-893]\t893\t9\n+COV\t[894-894]\t894\t12\n+COV\t[895-895]\t895\t16\n+COV\t[896-896]\t896\t10\n+COV\t[897-897]\t897\t8\n+COV\t[898-898]\t898\t8\n+COV\t[899-899]\t899\t11\n+COV\t[900-900]\t900\t7\n+COV\t[901-901]\t901\t15\n+COV\t[902-902]\t902\t13\n+COV\t[903-903]\t903\t17\n+COV\t[904-904]\t904\t9\n+COV\t[905-905]\t905\t8\n+COV\t[906-906]\t906\t13\n+COV\t[907-907]\t907\t10\n+COV\t[908-908]\t908\t8\n+COV\t[909-909]\t909\t13\n+COV\t[910-910]\t910\t7\n+COV\t[911-911]\t911\t9\n+COV\t[912-912]\t912\t8\n+COV\t[913-913]\t913\t9\n+COV\t[914-914]\t914\t8\n+COV\t[915-915]\t915\t9\n+COV\t[916-916]\t916\t6\n+COV\t[917-917]\t917\t9\n+COV\t[918-918]\t918\t7\n+COV\t[919-919]\t919\t9\n+COV\t[920-920]\t920\t8\n+COV\t[921-921]\t921\t13\n+COV\t[922-922]\t922\t5\n+COV\t[923-923]\t923\t5\n+COV\t[924-924]\t924\t5\n+COV\t[925-925]\t925\t7\n+COV\t[926-926]\t926\t10\n+COV\t[927-927]\t927\t6\n+COV\t[928-928]\t928\t21\n+COV\t[929-929]\t929\t10\n+COV\t[930-930]\t930\t10\n+COV\t[931-931]\t931\t7\n+COV\t[932-932]\t932\t12\n+COV\t[933-933]\t933\t14\n+COV\t[934-934]\t934\t14\n+COV\t[935-935]\t935\t7\n+COV\t[936-936]\t936\t12\n+COV\t[937-937]\t937\t13\n+COV\t[938-938]\t938\t10\n+COV\t[939-939]\t939\t12\n+COV\t[940-940]\t940\t18\n+COV\t[941-941]\t941\t11\n+COV\t[942-942]\t942\t10\n+COV\t[943-943]\t943\t6\n+COV\t[944-944]\t944\t12\n+COV\t[945-945]\t945\t12\n+COV\t[946-946]\t946\t8\n+COV\t[947-947]\t947\t12\n+COV\t[948-948]\t948\t10\n+COV\t[949-949]\t949\t5\n+COV\t[950-950]\t950\t9\n+COV\t[951-951]\t951\t16\n+COV\t[952-952]\t952\t13\n+COV\t[953-953]\t953\t15\n+COV\t[954-954]\t954\t15\n+COV\t[955-955]\t955\t8\n+COV\t[956-956]\t956\t15\n+COV\t[957-957]\t957\t18\n+COV\t[958-958]\t958\t9\n+COV\t[959-959]\t959\t21\n+COV\t[960-960]\t960\t14\n+COV\t[961-961]\t961\t17\n+COV\t[962-962]\t962\t9\n+COV\t[963-963]\t963\t14\n+COV\t[964-964]\t964\t6\n+COV\t[965-965]\t965\t5\n+COV\t[966-966]\t966\t13\n+COV\t[967-967]\t967\t12\n+COV\t[968-968]\t968\t13\n+COV\t[969-969]\t969\t10\n+COV\t[970-970]\t970\t13\n+COV\t[971-971]\t971\t8\n+COV\t[972-972]\t972\t13\n+COV\t[973-973]\t973\t12\n+COV\t[974-974]\t974\t14\n+COV\t[975-975]\t975\t9\n+COV\t[976-976]\t976\t12\n+COV\t[977-977]\t977\t4\n+COV\t[978-978]\t978\t14\n+COV\t[979-979]\t979\t6\n+COV\t[980-980]\t980\t12\n+COV\t[981-981]\t981\t5\n+COV\t[982-982]\t982\t8\n+COV\t[983-983]\t983\t4\n+COV\t[984-984]\t984\t9\n+COV\t[985-985]\t985\t9\n+COV\t[986-986]\t986\t10\n+COV\t[987-987]\t987\t8\n+COV\t[988-988]\t988\t4\n+COV\t[989-989]\t989\t6\n+COV\t[990-990]\t990\t3\n+COV\t[991-991]\t991\t5\n+COV\t[992-992]\t992\t2\n+COV\t[993-993]\t993\t6\n+COV\t[994-994]\t994\t6\n+COV\t[995-995]\t995\t7\n+COV\t[996-996]\t996\t14\n+COV\t[997-997]\t997\t12\n+COV\t[998-998]\t998\t7\n+COV\t[999-999]\t999\t8\n+COV\t[1000-1000]\t1000\t8\n+COV\t[1000<]\t1000\t5025\n+# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n+GCD\t0.0\t0.554\t0.000\t0.000\t0.000\t0.000\t0.000\n+GCD\t0.5\t0.831\t0.525\t0.525\t0.525\t0.525\t0.525\n+GCD\t36.0\t1.385\t0.954\t0.954\t0.954\t1.490\t1.490\n+GCD\t37.0\t2.216\t2.495\t2.495\t4.146\t6.560\t6.560\n+GCD\t38.0\t5.263\t0.247\t0.454\t3.520\t5.868\t9.883\n+GCD\t39.0\t9.141\t0.177\t0.303\t2.161\t8.777\t12.812\n+GCD\t40.0\t12.188\t0.020\t1.192\t9.060\t22.018\t27.371\n+GCD\t41.0\t16.343\t0.035\t0.550\t2.702\t11.469\t12.908\n+GCD\t42.0\t21.884\t0.010\t0.172\t2.121\t5.621\t17.094\n+GCD\t43.0\t28.255\t0.010\t0.328\t1.449\t4.277\t10.166\n+GCD\t44.0\t36.288\t0.162\t0.394\t5.484\t15.145\t50.490\n+GCD\t45.0\t42.105\t0.020\t0.131\t1.252\t7.009\t17.811\n+GCD\t46.0\t49.861\t0.015\t0.121\t0.636\t1.939\t37.506\n+GCD\t47.0\t56.510\t0.030\t0.141\t1.015\t4.500\t6.338\n+GCD\t48.0\t64.543\t0.010\t0.091\t2.565\t7.287\t21.872\n+GCD\t49.0\t68.975\t0.010\t0.333\t0.672\t10.751\t27.129\n+GCD\t50.0\t73.407\t0.010\t0.121\t1.358\t3.883\t6.615\n+GCD\t51.0\t77.008\t0.121\t0.576\t1.576\t4.363\t13.923\n+GCD\t52.0\t81.994\t0.010\t0.086\t1.560\t4.414\t109.383\n+GCD\t53.0\t84.488\t0.040\t0.071\t0.500\t3.025\t31.234\n+GCD\t54.0\t86.704\t0.020\t0.313\t9.332\t39.683\t203.959\n+GCD\t55.0\t89.197\t0.005\t0.051\t1.268\t5.045\t23.578\n+GCD\t56.0\t91.136\t0.071\t0.192\t1.566\t9.994\t33.315\n+GCD\t57.0\t94.460\t0.040\t0.348\t1.167\t5.050\t11.660\n+GCD\t58.0\t95.845\t0.131\t0.131\t1.899\t2.742\t4.929\n+GCD\t59.0\t96.399\t3.313\t3.313\t3.313\t3.666\t3.666\n+GCD\t60.0\t97.507\t0.995\t0.995\t5.176\t6.954\t33.234\n+GCD\t61.0\t98.338\t1.591\t1.591\t1.788\t4.848\t4.848\n+GCD\t62.0\t98.892\t3.171\t3.171\t3.171\t7.343\t7.343\n+GCD\t63.0\t99.446\t0.530\t0.530\t0.530\t6.403\t6.403\n+GCD\t64.0\t100.000\t1.025\t1.025\t1.025\t4.585\t4.585\n' |
| b |
| diff -r 000000000000 -r 8f25feb85166 test-data/tophat_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_data.txt Fri May 27 06:22:43 2016 -0400 |
| b |
| @@ -0,0 +1,14 @@ +Left reads: + Input : 316390 + Mapped : 314921 (99.5% of input) + of these: 5715 ( 1.8%) have multiple alignments (0 have >20) +Right reads: + Input : 316390 + Mapped : 314789 (99.5% of input) + of these: 5707 ( 1.8%) have multiple alignments (0 have >20) +99.5% overall read mapping rate. + +Aligned pairs: 313405 + of these: 5638 ( 1.8%) have multiple alignments + 34 ( 0.0%) are discordant alignments +99.0% concordant pair alignment rate. |
| b |
| diff -r 000000000000 -r 8f25feb85166 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri May 27 06:22:43 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="multiqc" version="0.6"> + <repository changeset_revision="ba145f5a7760" name="package_multiqc_0_6" owner="engineson" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |