| Previous changeset 7:467486f1c568 (2018-01-14) Next changeset 9:df99138d2776 (2018-04-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 |
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modified:
generate_test_data.sh multiqc.xml test-data/aligner_soft_stats.tabular test-data/bamtools_stats.tabular test-data/bcftools_stats.tabular test-data/bismark_stats.tabular test-data/bowtie2_stats.tabular test-data/busco_stats.tabular test-data/cutadapt_stats.tabular test-data/fastqc_stats.tabular test-data/featureCounts_stats.tabular test-data/flexbar_stats.tabular test-data/gatk_varianteval_stats.tabular test-data/hisat2_stats.tabular test-data/htseq_stats.tabular test-data/kallisto_stats.tabular test-data/picard_AlignmentSummaryMetrics_stats.tabular test-data/picard_RnaSeqMetrics_stats.tabular test-data/picard_baseContent_stats.tabular test-data/picard_dups_stats.tabular test-data/post_aligner_soft_stats.tabular test-data/pre_alignment_soft_log.txt test-data/pre_alignment_soft_stats.tabular test-data/prokka_stats.tabular test-data/quast_stats.tabular test-data/report_manual_custom_content.html test-data/samblaster_stats.tabular test-data/samtools_flagstat_stats.tabular test-data/samtools_stats_stats.tabular test-data/sortmerna_stats.tabular test-data/star_stats.tabular test-data/tophat_stats.tabular test-data/trimmomatic_stats.tabular |
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added:
test-data/aligner_soft_report.html test-data/deeptools_bamPEFragmentSize.txt test-data/deeptools_estimateReadFiltering.txt test-data/deeptools_plotCoverageOutRawCounts.txt test-data/deeptools_plotCoverageStdout.txt test-data/deeptools_plotEnrichment.txt test-data/deeptools_plotFingerprintOutRawCounts.txt test-data/post_aligner_soft_report.html test-data/pre_alignment_soft_report.html test-data/salmon_flenDist.txt test-data/salmon_meta_info.json test-data/snpeff_stats.tabular |
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removed:
test-data/salmon.txt |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 generate_test_data.sh --- a/generate_test_data.sh Sun Jan 14 09:55:46 2018 -0500 +++ b/generate_test_data.sh Fri Apr 20 01:06:25 2018 -0400 |
| b |
| b"@@ -1,25 +1,23 @@\n #!/usr/bin/env bash\n \n # 1st test\n-mkdir multiqc_WDir\n+mkdir -p 'multiqc_WDir/cutadapt'\n+cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt/cutadapt.txt'\n+sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt/cutadapt.txt'\n \n-mkdir 'multiqc_WDir/cutadapt_0'\n-cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt'\n-sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt'\n+mkdir -p 'multiqc_WDir/fastqc/data_0/file_0'\n+cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc/data_0/file_0/fastqc_data.txt'\n+mkdir -p 'multiqc_WDir/fastqc/data_0/file_1'\n+cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc/data_0/file_1/fastqc_data.txt'\n \n-mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0'\n-cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt'\n-mkdir 'multiqc_WDir/fastqc_1/data_0/file_1'\n-cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt'\n+mkdir -p 'multiqc_WDir/flexbar'\n+cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar/flexbar.txt'\n \n-mkdir 'multiqc_WDir/flexbar_2'\n-cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt'\n+mkdir -p 'multiqc_WDir/sortmerna'\n+cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna/sortmerna.txt'\n \n-mkdir 'multiqc_WDir/sortmerna_3'\n-cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt'\n-\n-mkdir 'multiqc_WDir/trimmomatic_4'\n-cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt'\n+mkdir -p 'multiqc_WDir/trimmomatic'\n+cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic/trimmomatic.txt'\n \n multiqc multiqc_WDir\n \n@@ -36,33 +34,37 @@\n rm -rf 'multiqc_data/'\n \n # 2nd test\n-mkdir multiqc_WDir\n+mkdir -p 'multiqc_WDir/bismark'\n+cp 'test-data/bismark.txt' 'multiqc_WDir/bismark/bismark_SE_report.txt'\n \n-mkdir 'multiqc_WDir/bismark_0'\n-cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt'\n+mkdir -p 'multiqc_WDir/bowtie2'\n+cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2/bowtie2_1.txt'\n+cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2/bowtie2_2.txt'\n \n-mkdir 'multiqc_WDir/bowtie2_1'\n-cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt'\n-cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt'\n+mkdir -p 'multiqc_WDir/hisat2'\n+cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2/hisat2_1.txt'\n+cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt'\n \n-mkdir 'multiqc_WDir/hisat2_3'\n-cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt'\n-cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt'\n+mkdir -p 'multiqc_WDir/hicexplorer'\n+cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/'\n+cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/'\n \n-mkdir 'multiqc_WDir/kallisto_4'\n-cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt'\n-cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt'\n-\n-mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0'\n-cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt'\n+mkdir -p 'multiqc_WDir/kallisto'\n+cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt'\n+cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto/kallisto_2.txt'\n \n-mkdir -p 'multiqc_WDir/star_6/log_0'\n-cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out'\n-mkdir 'multiqc_WDir/star_6/genecounts_1'\n-cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab'\n+#mkdir -p 'multiqc_WDir/salmon/fld_0/file_0'\n+#cp 'test-data/salmon_flenDist.txt' 'multiqc_WDir/salmon/fld_0/file_0/flenDist.txt'\n+#mkdir -p 'multiqc_WDir/salmon/fld_1/file_0'\n+#cp 'test-data/salmon_meta_info.json' 'multiqc_WDir/salmon/fld_1/file_0/meta_info.json'\n \n-mkdir 'multiqc_WDir/tophat_7'\n-cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt'\n+mkdir -p 'multiqc_WDir/star/log_0'\n+cp 'test-data/star_log.txt' 'multiqc_WDir/star/log_0/star_log_Log.final.out'\n+mkdir -p 'multiqc_WDir/star/genecounts_1'\n+c"..b"/picard'\n+cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard/picard_collectGcBias.txt'\n+cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard/picard_CollectInsertSizeMetrics.txt'\n+cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard/picard_MarkDuplicates.txt'\n+cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard/picard_CollectBaseDistributionByCycle.txt'\n+cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard/picard_CollectRnaSeqMetrics.txt'\n+cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard/picard_CollectAlignmentSummaryMetrics.txt'\n \n-mkdir -p 'multiqc_WDir/quast_8/file_0'\n-cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv'\n+mkdir -p 'multiqc_WDir/prokka'\n+cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka/prokka_1.txt'\n+cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka/prokka_2.txt'\n \n-#mkdir 'multiqc_WDir/rsem_9'\n-#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt'\n+mkdir -p 'multiqc_WDir/quast/file_0'\n+cp 'test-data/quast.tsv' 'multiqc_WDir/quast/file_0/report.tsv'\n \n-mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0'\n-cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls'\n+#mkdir -p 'multiqc_WDir/rsem'\n+#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem/rsem.cnt'\n \n-mkdir 'multiqc_WDir/samblaster_11'\n-cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt'\n+mkdir -p 'multiqc_WDir/rseqc/read_gc_0'\n+cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc/read_gc_0/rseq.GC.xls'\n+\n+mkdir -p 'multiqc_WDir/samblaster'\n+cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster/samblaster.txt'\n \n-mkdir -p 'multiqc_WDir/samtools_12/stats_0'\n-cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt'\n-mkdir 'multiqc_WDir/samtools_12/flagstat_1'\n-cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt'\n-mkdir 'multiqc_WDir/samtools_12/idxstats_2'\n-cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat'\n+mkdir -p 'multiqc_WDir/samtools/stats_0'\n+cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools/stats_0/samtools_stats.txt'\n+mkdir -p 'multiqc_WDir/samtools/flagstat_1'\n+cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/flagstat_1/samtools_flagstat.txt'\n+mkdir -p 'multiqc_WDir/samtools/idxstats_2'\n+cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/idxstats_2/samtools_idxstats_idxstat'\n \n-#mkdir 'multiqc_WDir/snpeff_13'\n-#cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt'\n+mkdir -p 'multiqc_WDir/snpeff'\n+cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff/snpeff.txt'\n \n-mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0'\n-cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual'\n+mkdir -p 'multiqc_WDir/vcftools/tstv_by_qual_0'\n+cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools/tstv_by_qual_0/vcftools.TsTv.qual'\n \n multiqc multiqc_WDir\n \n@@ -155,19 +163,16 @@\n mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular'\n mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular'\n #mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular'\n-mv 'multiqc_data/multiqc_rseqc.txt' 'test-data/rseqc_stats.tabular'\n mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular'\n mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular'\n mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular'\n-#mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'\n+mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'\n \n rm -rf 'multiqc_WDir'\n rm -rf 'multiqc_data/'\n \n # 4th test\n-mkdir multiqc_WDir\n-\n-mkdir 'multiqc_WDir/custom_content_0'\n+mkdir -p 'multiqc_WDir/custom_content_0'\n cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv'\n cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv'\n \n" |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 multiqc.xml --- a/multiqc.xml Sun Jan 14 09:55:46 2018 -0500 +++ b/multiqc.xml Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b'@@ -1,26 +1,49 @@\n-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">\n+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.0">\n <description>aggregate results from bioinformatics analyses into a single report</description>\n <macros>\n- <token name="@WRAPPER_VERSION@">1.3</token>\n+ <token name="@WRAPPER_VERSION@">1.5</token>\n+ <token name="@ESCAPE_IDENTIFIER@">\n+<![CDATA[\n+#set identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($file.element_identifier))\n+ ]]></token>\n+ <token name="@CHECK_LN_FILE@">\n+<![CDATA[\n+grep -q "$pattern" $file || die "Module \'${repeat.software_cond.software}: \'$pattern\' not found in the file \'$identifier\'" &&\n+ln -s \'$file\' \'$file_path\' &&\n+ ]]></token>\n+ <token name="@CREATE_REPEAT_DIR_1@">\n+<![CDATA[\n+#set repeat_dir = os.path.join($software_dir, str($repeat2.type) + \'_\' + str($j))\n+mkdir \'$repeat_dir\' &&\n+ ]]></token>\n+ <token name="@CREATE_REPEAT_DIR_2@">\n+<![CDATA[\n+#set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + \'_\' + str($j))\n+mkdir \'$repeat_dir\' &&\n+ ]]></token>\n <token name="@LN_FILES@">\n <![CDATA[\n #for $file in $repeat.software_cond.input\n- grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n- ln -s \'$file\' \'$software_dir/${file.element_identifier}\' &&\n+ @ESCAPE_IDENTIFIER@\n+ #set file_path = os.path.join($software_dir, str($identifier))\n+ @CHECK_LN_FILE@\n #end for\n ]]></token>\n <token name="@LN_2_FILES@">\n <![CDATA[\n-#for $file in $repeat2.input:\n- grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n- ln -s \'$file\' \'$software_dir/${repeat2.type}_${j}_${file.element_identifier}\' &&\n+@CREATE_REPEAT_DIR_1@\n+#for $file in $repeat2.input\n+ #set identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($file.element_identifier))\n+ #set file_path = os.path.join($repeat_dir, str($identifier))\n+ @CHECK_LN_FILE@\n #end for\n ]]></token>\n <token name="@LN_3_FILES@">\n <![CDATA[\n-#for $file in $repeat2.type.input:\n- grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n- ln -s \'$file\' \'$repeat_dir/${file.element_identifier}\' &&\n+#for $file in $repeat2.type.input\n+ #set identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($file.element_identifier))\n+ #set file_path = os.path.join($repeat_dir, str($identifier))\n+ @CHECK_LN_FILE@\n #end for\n ]]></token>\n </macros>\n@@ -30,6 +53,9 @@\n <version_command>multiqc --version</version_command>\n <command detect_errors="aggressive">\n <![CDATA[\n+#import re\n+#import os\n+\n die() { echo "$@" 1>&2 ; exit 1; } &&\n \n mkdir multiqc_WDir &&\n@@ -37,7 +63,7 @@\n #set $configfile="F"\n \n #for $i, $repeat in enumerate( $results )\n- #set software_dir = \'multiqc_WDir/\' + str($repeat.software_cond.software) + \'_\' + str($i)\n+ #set software_dir = os.path.join(\'multiqc_WDir\', str($repeat.software_cond.software) + \'_\' + str($i))\n mkdir $software_dir &&\n \n #if str($repeat.software_cond.software) == "bamtools"\n@@ -48,26 +74,36 @@\n @LN_FILES@\n #elif str($repeat.software_cond.software) == "bismark"\n #for $j, $repeat2 in enumerate( $repeat.software_cond.output )\n- #set file_prefix = $software_dir + \'/\' + str($repeat2.type) + \'_\' + str($j)\n+ @CREATE_REPEAT_DIR_1@\n #if str($repeat2.type) == "align"\n #for $file in $repeat2.input\n- ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_SE_report.txt\' &&\n+ @ESCAPE_IDENTIFIER@\n+ #set file_path = os.path.join($repeat_dir, str($identifier) + \'_SE_report.txt\')\n+ ln -s \'$file\' \'$file_path\' &&\n #end for\n #elif str($repeat2.type) == "dedup"\n #for $file in $repeat2.input\n- ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_deduplication_report.txt\' &&\n+ @ESCAPE_IDENTIFIE'..b'e="software" value="featureCounts" />\n <param name="input" value="featureCounts.txt" />\n </conditional>\n@@ -921,6 +1080,12 @@\n </repeat>\n <repeat name="results">\n <conditional name="software_cond">\n+ <param name="software" value="snpeff" />\n+ <param name="input" value="snpeff.csv" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="results">\n+ <conditional name="software_cond">\n <param name="software" value="vcftools" />\n <repeat name="output">\n <conditional name="type">\n@@ -936,6 +1101,7 @@\n <has_text text="bamtools-stats" />\n <has_text text="bcftools_stats_indel-lengths" />\n <has_text text="busco-lineage-fungi_odb9" />\n+ <has_text text="deeptools" />\n <has_text text="featureCounts_assignment_plot" />\n <has_text text="gatk_varianteval_variant_plot" />\n <has_text text="htseq_assignment_plot" />\n@@ -948,17 +1114,17 @@\n <has_text text="samblaster_duplicates" />\n <has_text text="quast-stats" />\n <has_text text="samtools-flagstat-dp" />\n- <has_text text="bamtools-stats" />\n+ <has_text text="snpeff" />\n </assert_contents>\n </output>\n <output_collection name="stats" type="list">\n- <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>\n <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>\n- <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>\n <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>\n <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>\n <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/>\n- <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/>\n <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/>\n <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>\n <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>\n@@ -975,6 +1141,7 @@\n </assert_contents>\n </element>\n <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>\n+ <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>\n </output_collection>\n </test>\n <test>\n@@ -1005,7 +1172,7 @@\n \n ----\n \n-The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility).\n+The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.\n ]]></help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btw354</citation>\n' |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/aligner_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligner_soft_report.html Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b'@@ -0,0 +1,5608 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+<!--\n+ __ __ _ _ _ ___ ____\n+ | \\/ |_ _| | |_(_)/ _ \\ / ___|\n+ | |\\/| | | | | | __| | | | | |\n+ | | | | |_| | | |_| | |_| | |___\n+ |_| |_|\\__,_|_|\\__|_|\\__\\_\\\\____|\n+\n+Abandon hope all ye who enter here..\n+http://multiqc.info\n+-->\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+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\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+\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 467486f1c568 -r e0f4a651c6b9 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/aligner_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,16 +1,16 @@ -Sample Cutadapt_percent_trimmed-1 Kallisto_percent_aligned-1-1 Kallisto_pseudoaligned_reads-1 Kallisto_fragment_length-1 Bismark_aligned_reads-1 Bismark_percent_aligned-2 Bowtie 2_overall_alignment_rate-1-1 HiCExplorer_Pairs_considered-1 HiCExplorer_Min_rest_site_distance-1 HiCExplorer_Mapped-1 HiCExplorer_Max_rest_site_distance-1 HiCExplorer_Pairs_used-1 HISAT2_overall_alignment_rate-2 STAR_uniquely_mapped_percent-1 STAR_uniquely_mapped-1 Tophat_overall_aligned_percent-1 Tophat_aligned_not_multimapped_discordant-1 +Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-pseudoaligned_reads Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-percent_aligned Bismark_mqc-generalstats-aligned_reads Bismark_mqc-generalstats-percent_aligned Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Min_rest_site_distance HiCExplorer_mqc-generalstats-Pairs_considered HiCExplorer_mqc-generalstats-Max_rest_site_distance HISAT2_mqc-generalstats-overall_alignment_rate STAR_mqc-generalstats-uniquely_mapped_percent STAR_mqc-generalstats-uniquely_mapped Tophat_mqc-generalstats-overall_aligned_percent Tophat_mqc-generalstats-aligned_not_multimapped_discordant HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 48531088.0 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 167.866 83.65114569077758 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 59280920.0 169.418 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 169.418 84.50278473550448 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -align_0 220558.0 69.71079996207212 +bismark_SE_report 220558.0 69.71079996207212 bowtie2_1 98.33 bowtie2_2 98.31 -hicexplorer_3_small_test 99983.0 303.0 0.08778492343698428 800.0 0.3732734564876029 -hicexplorer_3_small_test_rf 99983.0 152.0 0.08778492343698428 1500.0 0.35940109818669175 +hicexplorer_hicexplorer1_small_test 0.08778492343698428 0.3732734564876029 303.0 99983.0 800.0 +hicexplorer_hicexplorer2_small_test_rf 0.08778492343698428 0.35940109818669175 152.0 99983.0 1500.0 hisat2_1 96.15 hisat2_2 96.15 star_log 89.0 89.0 -tophat 99.5 307733.0 +tophat_align 99.5 307733.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bamtools_stats.tabular --- a/test-data/bamtools_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bamtools_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample mapped_reads mapped_reads_pct forward_strand_pct read_2 read_1 duplicates both_mapped reverse_strand_pct duplicates_pct reverse_strand forward_strand failed_qc_pct both_mapped_pct failed_qc singletons total_reads singletons_pct paired_end paired_end_pct -bamtools 316585701.0 93.125 53.4381 169978965.0 169978965.0 0.0 314020716.0 46.5619 0.0 158290963.0 181666967.0 0.0 92.3705 0.0 2564985.0 339957930.0 0.754501 339957930.0 100.0 +Sample total_reads forward_strand mapped_reads both_mapped_pct read_1 mapped_reads_pct failed_qc_pct forward_strand_pct reverse_strand paired_end paired_end_pct duplicates_pct singletons read_2 both_mapped failed_qc reverse_strand_pct singletons_pct duplicates +bamtools 339957930.0 181666967.0 316585701.0 92.3705 169978965.0 93.125 0.0 53.4381 158290963.0 339957930.0 100.0 0.0 2564985.0 169978965.0 314020716.0 0.0 46.5619 0.754501 0.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bcftools_stats.tabular --- a/test-data/bcftools_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bcftools_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample number_of_records ts_1st_ALT substitution_type_G>C tv substitution_type_A>G substitution_type_A>C number_of_multiallelic_SNP_sites number_of_multiallelic_sites substitution_type_A>T number_of_SNPs number_of_MNPs substitution_type_T>G tstv_1st_ALT tstv number_of_no-ALTs substitution_type_C>G substitution_type_C>T ts number_of_samples substitution_type_T>C substitution_type_G>T substitution_type_T>A substitution_type_C>A number_of_indels tv_1st_ALT number_of_others substitution_type_G>A -Test1 5522770.0 2968539.0 197866.0 1505704.0 721395.0 190164.0 0.0 0.0 166827.0 4474244.0 72330.0 189578.0 1.97 1.97 0.0 197211.0 762114.0 2968539.0 1.0 721436.0 201005.0 166222.0 196831.0 902934.0 1505704.0 73262.0 763594.0 +Sample number_of_samples tstv substitution_type_C>T substitution_type_A>C substitution_type_T>C number_of_multiallelic_sites tv_1st_ALT substitution_type_A>T substitution_type_A>G substitution_type_T>A ts number_of_multiallelic_SNP_sites substitution_type_C>A substitution_type_G>A substitution_type_G>C number_of_MNPs tstv_1st_ALT number_of_records number_of_others tv number_of_SNPs number_of_indels number_of_no-ALTs substitution_type_T>G substitution_type_C>G substitution_type_G>T ts_1st_ALT +Test1 1.0 1.97 762114.0 190164.0 721436.0 0.0 1505704.0 166827.0 721395.0 166222.0 2968539.0 0.0 196831.0 763594.0 197866.0 72330.0 1.97 5522770.0 73262.0 1505704.0 4474244.0 902934.0 0.0 189578.0 197211.0 201005.0 2968539.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bismark_stats.tabular --- a/test-data/bismark_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bismark_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg -align_0 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 +bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bowtie2_stats.tabular --- a/test-data/bowtie2_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bowtie2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ -Sample overall_alignment_rate unpaired_total unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi total_reads -bowtie2_1 98.33 21040602 13299463 351563 7389576 21040602 -bowtie2_2 98.31 16199126 10087714 274008 5837404 16199126 +Sample unpaired_total unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none total_reads unpaired_aligned_one +bowtie2_1 21040602 7389576 98.33 351563 21040602 13299463 +bowtie2_2 16199126 5837404 98.31 274008 16199126 10087714 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/busco_stats.tabular --- a/test-data/busco_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/busco_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample fragmented complete missing complete_single_copy total lineage_dataset complete_duplicated -short 5.0 257.0 28.0 255.0 290.0 fungi_odb9 2.0 +Sample fragmented complete_single_copy total complete missing lineage_dataset complete_duplicated +busco 5.0 255.0 290.0 257.0 28.0 fungi_odb9 2.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/cutadapt_stats.tabular --- a/test-data/cutadapt_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/cutadapt_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample too_short percent_trimmed too_long bp_trimmed bp_processed r_trimmed r_processed -dataset_33 0 10.776820436239396 0 3443775 31955390 68795 316390 +Sample r_trimmed percent_trimmed too_long too_short r_processed bp_processed bp_trimmed +dataset_33 68795 10.776820436239396 0 0 316390 31955390 3443775 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_bamPEFragmentSize.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_bamPEFragmentSize.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ + Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99% +bwameth_se.pbat.bam 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51142 40.0 101.0 98.0356654022 101.0 101.0 101.0 10.864939372 0.0 99.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 +bismark_se.pbat.bam 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34118 21.0 101.0 99.5840905094 101.0 101.0 101.0 7.089489864 0.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_1_RGi.bam 15504 174.0 185.0 184.99245356 185.0 185.0 186.0 0.175975291035 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 15504 148.0 148.0 148.0 148.0 148.0 148.0 0.0 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_2_RGi.bam 17327 176.0 185.0 184.989957869 185.0 185.0 186.0 0.19282636998 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 17327 148.0 148.0 148.0 148.0 148.0 148.0 0.0 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_3_RGi.bam 15266 104.0 185.0 184.98545788 185.0 185.0 186.0 0.676996184607 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 15266 102.0 148.0 147.996986768 148.0 148.0 148.0 0.372289663166 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_estimateReadFiltering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_estimateReadFiltering.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Sample Total Reads Mapped Reads Alignments in blacklisted regions Estimated mapped reads filtered Below MAPQ Missing Flags Excluded Flags Internally-determined Duplicates Marked Duplicates Singletons Wrong strand +bwameth_se.pbat.bam 71373361 46192726 0 14151494.8 5163035.6 0.0 0.0 20264594.9 0.0 0.0 4596084.6 +bismark_se.pbat.bam 30924955 30924955 0 13624010.0 10983580.2 0.0 0.0 13414682.1 0.0 0.0 1542611.8 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotCoverageOutRawCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotCoverageOutRawCounts.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| b"@@ -0,0 +1,20000 @@\n+#plotCoverage --outRawCounts\n+#'chr'\t'start'\t'end'\t'bwameth_se.pbat.bam'\t'bismark_se.pbat.bam'\n+KI270589.1\t43386\t43387\t4.0\t0.0\n+13\t16229463\t16229464\t1.0\t0.0\n+13\t16257354\t16257355\t1.0\t0.0\n+13\t16306938\t16306939\t1.0\t0.0\n+13\t16430898\t16430899\t1.0\t0.0\n+13\t16554858\t16554859\t1.0\t0.0\n+13\t16604442\t16604443\t2.0\t0.0\n+13\t16787283\t16787284\t1.0\t0.0\n+13\t16812075\t16812076\t1.0\t0.0\n+13\t16821372\t16821373\t1.0\t0.0\n+13\t16880253\t16880254\t1.0\t0.0\n+13\t16892649\t16892650\t1.0\t0.0\n+13\t16929837\t16929838\t1.0\t0.0\n+13\t17156064\t17156065\t1.0\t0.0\n+13\t17187054\t17187055\t1.0\t0.0\n+13\t17301717\t17301718\t1.0\t0.0\n+13\t17326509\t17326510\t1.0\t0.0\n+13\t17422578\t17422579\t1.0\t0.0\n+13\t17434974\t17434975\t1.0\t0.0\n+13\t17450469\t17450470\t1.0\t0.0\n+13\t17549637\t17549638\t1.0\t0.0\n+13\t17599221\t17599222\t1.0\t0.0\n+13\t17633310\t17633311\t1.0\t0.0\n+13\t17645706\t17645707\t1.0\t0.0\n+13\t17673597\t17673598\t1.0\t0.0\n+13\t17754171\t17754172\t1.0\t0.0\n+13\t17909121\t17909122\t1.0\t0.0\n+13\t18191130\t18191131\t18.0\t7.0\n+13\t18194229\t18194230\t95.0\t24.0\n+13\t18197328\t18197329\t1.0\t1.0\n+13\t18200427\t18200428\t1.0\t0.0\n+13\t18206625\t18206626\t3.0\t1.0\n+13\t18212823\t18212824\t1.0\t0.0\n+13\t18231417\t18231418\t1.0\t0.0\n+13\t18234516\t18234517\t1.0\t0.0\n+13\t18256209\t18256210\t2.0\t0.0\n+13\t18265506\t18265507\t1.0\t2.0\n+13\t18268605\t18268606\t1.0\t0.0\n+13\t18274803\t18274804\t14.0\t7.0\n+13\t18277902\t18277903\t9.0\t6.0\n+13\t18281001\t18281002\t1.0\t0.0\n+13\t18290298\t18290299\t23.0\t0.0\n+13\t18296496\t18296497\t11.0\t0.0\n+13\t18299595\t18299596\t12.0\t6.0\n+13\t18302694\t18302695\t22.0\t8.0\n+13\t18311991\t18311992\t4.0\t0.0\n+13\t18324387\t18324388\t33.0\t13.0\n+13\t18336783\t18336784\t1.0\t0.0\n+13\t18408060\t18408061\t5.0\t2.0\n+13\t18420456\t18420457\t3.0\t0.0\n+13\t18423555\t18423556\t5.0\t0.0\n+13\t18435951\t18435952\t1.0\t0.0\n+13\t18476238\t18476239\t1.0\t1.0\n+13\t18485535\t18485536\t1.0\t0.0\n+13\t18525822\t18525823\t1.0\t0.0\n+13\t18547515\t18547516\t1.0\t0.0\n+13\t18609495\t18609496\t3.0\t1.0\n+13\t18612594\t18612595\t4.0\t4.0\n+13\t18621891\t18621892\t1.0\t0.0\n+13\t18659079\t18659080\t1.0\t0.0\n+13\t18665277\t18665278\t2.0\t1.0\n+13\t18674574\t18674575\t3.0\t0.0\n+13\t18680772\t18680773\t3.0\t1.0\n+13\t18727257\t18727258\t17.0\t10.0\n+13\t18736554\t18736555\t1.0\t0.0\n+13\t18745851\t18745852\t1.0\t0.0\n+13\t18748950\t18748951\t1.0\t1.0\n+13\t18773742\t18773743\t1.0\t0.0\n+13\t18779940\t18779941\t1.0\t0.0\n+13\t18795435\t18795436\t1.0\t0.0\n+13\t18798534\t18798535\t2.0\t2.0\n+13\t18807831\t18807832\t3.0\t1.0\n+13\t18810930\t18810931\t1.0\t0.0\n+13\t18814029\t18814030\t2.0\t0.0\n+13\t18848118\t18848119\t1.0\t0.0\n+13\t18869811\t18869812\t1.0\t1.0\n+13\t18888405\t18888406\t4.0\t0.0\n+13\t18894603\t18894604\t12.0\t8.0\n+13\t18900801\t18900802\t2.0\t1.0\n+13\t18903900\t18903901\t1.0\t0.0\n+13\t18916296\t18916297\t2.0\t0.0\n+13\t18944187\t18944188\t39.0\t19.0\n+13\t18953484\t18953485\t21.0\t14.0\n+13\t18962781\t18962782\t19.0\t8.0\n+13\t18972078\t18972079\t1.0\t0.0\n+13\t19003068\t19003069\t2.0\t0.0\n+13\t19009266\t19009267\t8.0\t4.0\n+13\t19012365\t19012366\t1.0\t1.0\n+13\t19061949\t19061950\t3.0\t2.0\n+13\t19068147\t19068148\t7.0\t0.0\n+13\t19089840\t19089841\t2.0\t2.0\n+13\t19117731\t19117732\t8.0\t6.0\n+13\t19120830\t19120831\t1.0\t1.0\n+13\t19123929\t19123930\t1.0\t1.0\n+13\t19151820\t19151821\t1.0\t1.0\n+13\t19154919\t19154920\t10.0\t6.0\n+13\t19170414\t19170415\t13.0\t8.0\n+13\t19173513\t19173514\t14.0\t8.0\n+13\t19179711\t19179712\t61.0\t47.0\n+13\t19182810\t19182811\t5.0\t1.0\n+13\t19185909\t19185910\t8.0\t5.0\n+13\t19198305\t19198306\t7.0\t0.0\n+13\t19226196\t19226197\t1.0\t0.0\n+13\t19229295\t19229296\t2.0\t0.0\n+13\t19241691\t19241692\t2.0\t2.0\n+13\t19263384\t19263385\t110.0\t75.0\n+13\t19275780\t19275781\t4.0\t0.0\n+13\t19278879\t19278880\t1.0\t0.0\n+13\t19306770\t19306771\t2.0\t0.0\n+13\t19322265\t19322266\t1.0\t0.0\n+13\t19340859\t19340860\t7.0\t6.0\n+13\t19343958\t19343959\t1.0\t1.0\n+13\t19347057\t19347058\t137.0\t108.0\n+13\t19356354\t19356355\t1.0\t1.0\n+13\t19381146\t19381147\t10.0\t7.0\n+13\t19402839\t19402840\t1.0\t1.0\n+13\t19405938\t19405939\t1.0\t1.0\n+13\t19412136\t19412137\t2.0\t0.0\n+13\t19415235\t19415236\t1.0\t0.0\n+13\t19458621\t19458622\t10.0\t1.0\n+13\t19489611\t19489612\t2.0\t0.0\n+13\t19557789\t19557790\t10.0\t9.0\n+13\t19560888\t19560889\t6.0\t4.0\n+13\t19563987\t19563988\t26.0\t4.0\n+13\t19570185\t19570186\t1.0\t0.0\n+13\t19582581\t19582582\t3.0\t0.0\n+13\t19585680\t19585681\t2.0\t1.0\n+13\t19601175\t19601176\t4.0\t1.0\n+13\t196"..b'862606\t1.0\t0.0\n+15\t36868803\t36868804\t15.0\t14.0\n+15\t36878100\t36878101\t150.0\t116.0\n+15\t36881199\t36881200\t35.0\t18.0\n+15\t36884298\t36884299\t81.0\t57.0\n+15\t36887397\t36887398\t66.0\t36.0\n+15\t36896694\t36896695\t34.0\t29.0\n+15\t36909090\t36909091\t1.0\t0.0\n+15\t36912189\t36912190\t9.0\t2.0\n+15\t36933882\t36933883\t3.0\t1.0\n+15\t36946278\t36946279\t3.0\t1.0\n+15\t36952476\t36952477\t1.0\t1.0\n+15\t36977268\t36977269\t1.0\t0.0\n+15\t36992763\t36992764\t2.0\t2.0\n+15\t36995862\t36995863\t1.0\t0.0\n+15\t37020654\t37020655\t1.0\t0.0\n+15\t37023753\t37023754\t14.0\t0.0\n+15\t37029951\t37029952\t3.0\t1.0\n+15\t37057842\t37057843\t108.0\t84.0\n+15\t37082634\t37082635\t119.0\t100.0\n+15\t37085733\t37085734\t1.0\t0.0\n+15\t37091931\t37091932\t29.0\t11.0\n+15\t37095030\t37095031\t91.0\t71.0\n+15\t37098129\t37098130\t28.0\t12.0\n+15\t37101228\t37101229\t35.0\t19.0\n+15\t37104327\t37104328\t129.0\t92.0\n+15\t37107426\t37107427\t14.0\t6.0\n+15\t37110525\t37110526\t84.0\t66.0\n+15\t37113624\t37113625\t17.0\t13.0\n+15\t37119822\t37119823\t2.0\t0.0\n+15\t37135317\t37135318\t84.0\t66.0\n+15\t37163208\t37163209\t1.0\t0.0\n+15\t37197297\t37197298\t14.0\t0.0\n+15\t37491702\t37491703\t1.0\t1.0\n+15\t37510296\t37510297\t0.0\t1.0\n+15\t37519593\t37519594\t1.0\t0.0\n+15\t37550583\t37550584\t1.0\t1.0\n+15\t37569177\t37569178\t1.0\t1.0\n+15\t37671444\t37671445\t1.0\t0.0\n+15\t37680741\t37680742\t5.0\t0.0\n+15\t37711731\t37711732\t11.0\t0.0\n+15\t37739622\t37739623\t3.0\t0.0\n+15\t37752018\t37752019\t1.0\t0.0\n+15\t37773711\t37773712\t4.0\t0.0\n+15\t37795404\t37795405\t1.0\t1.0\n+15\t37823295\t37823296\t1.0\t1.0\n+15\t37826394\t37826395\t1.0\t1.0\n+15\t37844988\t37844989\t1.0\t1.0\n+15\t37879077\t37879078\t5.0\t0.0\n+15\t37891473\t37891474\t3.0\t2.0\n+15\t37900770\t37900771\t42.0\t27.0\n+15\t37934859\t37934860\t40.0\t19.0\n+15\t37941057\t37941058\t43.0\t31.0\n+15\t37984443\t37984444\t16.0\t14.0\n+15\t38037126\t38037127\t1.0\t1.0\n+15\t38068116\t38068117\t1.0\t1.0\n+15\t38071215\t38071216\t1.0\t0.0\n+15\t38077413\t38077414\t1.0\t0.0\n+15\t38086710\t38086711\t1.0\t0.0\n+15\t38102205\t38102206\t1.0\t1.0\n+15\t38130096\t38130097\t52.0\t30.0\n+15\t38244759\t38244760\t0.0\t1.0\n+15\t38250957\t38250958\t92.0\t75.0\n+15\t38254056\t38254057\t6.0\t6.0\n+15\t38263353\t38263354\t3.0\t3.0\n+15\t38288145\t38288146\t1.0\t1.0\n+15\t38306739\t38306740\t1.0\t0.0\n+15\t38350125\t38350126\t1.0\t1.0\n+15\t38378016\t38378017\t40.0\t31.0\n+15\t38390412\t38390413\t1.0\t1.0\n+15\t38396610\t38396611\t11.0\t0.0\n+15\t38412105\t38412106\t1.0\t0.0\n+15\t38455491\t38455492\t27.0\t14.0\n+15\t38458590\t38458591\t13.0\t9.0\n+15\t38470986\t38470987\t2.0\t0.0\n+15\t38486481\t38486482\t1.0\t1.0\n+15\t38514372\t38514373\t1.0\t0.0\n+15\t38536065\t38536066\t25.0\t22.0\n+15\t38563956\t38563957\t96.0\t79.0\n+15\t38616639\t38616640\t1.0\t0.0\n+15\t38619738\t38619739\t7.0\t3.0\n+15\t38694114\t38694115\t1.0\t1.0\n+15\t38697213\t38697214\t80.0\t61.0\n+15\t38715807\t38715808\t1.0\t0.0\n+15\t38722005\t38722006\t2.0\t2.0\n+15\t38749896\t38749897\t3.0\t0.0\n+15\t38818074\t38818075\t13.0\t6.0\n+15\t38842866\t38842867\t3.0\t3.0\n+15\t38845965\t38845966\t3.0\t3.0\n+15\t38852163\t38852164\t1.0\t0.0\n+15\t38867658\t38867659\t0.0\t1.0\n+15\t38873856\t38873857\t2.0\t0.0\n+15\t38876955\t38876956\t19.0\t14.0\n+15\t38883153\t38883154\t9.0\t0.0\n+15\t38892450\t38892451\t7.0\t0.0\n+15\t38926539\t38926540\t1.0\t0.0\n+15\t38935836\t38935837\t1.0\t0.0\n+15\t38960628\t38960629\t1.0\t0.0\n+15\t38963727\t38963728\t1.0\t1.0\n+15\t38985420\t38985421\t1.0\t0.0\n+15\t38991618\t38991619\t7.0\t7.0\n+15\t38994717\t38994718\t7.0\t6.0\n+15\t39000915\t39000916\t1.0\t1.0\n+15\t39013311\t39013312\t2.0\t2.0\n+15\t39047400\t39047401\t1.0\t0.0\n+15\t39059796\t39059797\t1.0\t0.0\n+15\t39075291\t39075292\t1.0\t0.0\n+15\t39084588\t39084589\t1.0\t0.0\n+15\t39115578\t39115579\t2.0\t1.0\n+15\t39124875\t39124876\t10.0\t1.0\n+15\t39140370\t39140371\t11.0\t9.0\n+15\t39162063\t39162064\t1.0\t1.0\n+15\t39165162\t39165163\t12.0\t10.0\n+15\t39171360\t39171361\t1.0\t0.0\n+15\t39186855\t39186856\t3.0\t0.0\n+15\t39193053\t39193054\t5.0\t1.0\n+15\t39199251\t39199252\t2.0\t1.0\n+15\t39214746\t39214747\t1.0\t1.0\n+15\t39230241\t39230242\t4.0\t4.0\n+15\t39251934\t39251935\t44.0\t31.0\n+15\t39261231\t39261232\t10.0\t0.0\n+15\t39270528\t39270529\t5.0\t3.0\n+15\t39276726\t39276727\t37.0\t23.0\n+15\t39317013\t39317014\t61.0\t46.0\n+15\t39320112\t39320113\t1.0\t1.0\n+15\t39332508\t39332509\t23.0\t14.0\n+15\t39372795\t39372796\t1.0\t0.0\n+15\t39434775\t39434776\t18.0\t11.0\n+15\t39447171\t39447172\t1.0\t1.0\n+15\t39450270\t39450271\t1.0\t0.0\n+15\t39475062\t39475063\t4.0\t0.0\n' |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotCoverageStdout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotCoverageStdout.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +sample mean std min 25% 50% 75% max +bwameth_se.pbat.bam 4.48 23.43 0 0.0 0.0 0.0 2589 +bismark_se.pbat.bam 3.00 16.46 0 0.0 0.0 0.0 959 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotEnrichment.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotEnrichment.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -0,0 +1,17 @@ +file featureType percent featureReadCount totalReadCount +bwameth_se.pbat.bam gene 75.58 34911152 46192726 +bwameth_se.pbat.bam Selenocysteine 0.00 820 46192726 +bwameth_se.pbat.bam UTR 13.66 6308386 46192726 +bwameth_se.pbat.bam exon 31.37 14488419 46192726 +bwameth_se.pbat.bam stop_codon 0.76 352502 46192726 +bwameth_se.pbat.bam CDS 13.84 6395119 46192726 +bwameth_se.pbat.bam start_codon 1.49 687421 46192726 +bwameth_se.pbat.bam transcript 75.58 34910782 46192726 +bismark_se.pbat.bam gene 77.05 23828612 30924955 +bismark_se.pbat.bam Selenocysteine 0.00 667 30924955 +bismark_se.pbat.bam UTR 14.53 4492824 30924955 +bismark_se.pbat.bam exon 33.06 10224247 30924955 +bismark_se.pbat.bam stop_codon 0.86 266447 30924955 +bismark_se.pbat.bam CDS 14.94 4618943 30924955 +bismark_se.pbat.bam start_codon 1.65 509377 30924955 +bismark_se.pbat.bam transcript 77.05 23828340 30924955 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotFingerprintOutRawCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotFingerprintOutRawCounts.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
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|
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/fastqc_stats.tabular --- a/test-data/fastqc_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/fastqc_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ -Sample per_base_sequence_quality total_deduplicated_percentage sequence_duplication_levels basic_statistics Filename sequence_length_distribution avg_sequence_length per_sequence_quality_scores per_base_sequence_content adapter_content Total Sequences per_sequence_gc_content File type Encoding per_tile_sequence_quality per_base_n_content kmer_content Sequences flagged as poor quality Sequence length overrepresented_sequences %GC -poulet5_1 warn 63.69408840068983 warn pass poulet5_1 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 -poulet5_2 warn 63.826611251945884 warn pass poulet5_2 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 +Sample Filename File type Total Sequences sequence_duplication_levels overrepresented_sequences per_base_sequence_content per_base_sequence_quality per_base_n_content sequence_length_distribution %GC Encoding total_deduplicated_percentage per_sequence_quality_scores per_tile_sequence_quality Sequence length avg_sequence_length per_sequence_gc_content basic_statistics adapter_content Sequences flagged as poor quality kmer_content +poulet5_1 poulet5_1 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.69408840068983 warn pass 101.0 101.0 pass pass pass 0.0 warn +poulet5_2 poulet5_2 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.826611251945884 warn pass 101.0 101.0 pass pass pass 0.0 warn |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/featureCounts_stats.tabular --- a/test-data/featureCounts_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/featureCounts_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,7 +1,7 @@ -Sample Unassigned_Nonjunction percent_assigned Total Unassigned_FragmentLength Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Secondary Unassigned_MappingQuality Unassigned_Duplicate Unassigned_Ambiguity Unassigned_Unmapped Assigned Unassigned_Chimera -70: TopHat on data 1, data 4, and data 3: accepted_hits 0 70.82267755353567 454370 0 19123 111117 0 0 0 2333 0 321797 0 -75: TopHat on data 1, data 6, and data 5: accepted_hits 0 69.58585803304067 639515 0 25293 165786 0 0 0 3424 0 445012 0 -80: TopHat on data 1, data 8, and data 7: accepted_hits 0 71.76957768385707 550346 0 22580 129664 0 0 0 3121 0 394981 0 -85: TopHat on data 1, data 10, and data 9: accepted_hits 0 72.02454351337069 607411 0 19907 146327 0 0 0 3692 0 437485 0 -90: TopHat on data 1, data 12, and data 11: accepted_hits 0 71.33130826437625 544179 0 21164 132063 0 0 0 2782 0 388170 0 -95: TopHat on data 1, data 14, and data 13: accepted_hits 0 70.72517103678439 641821 0 23533 160805 0 0 0 3554 0 453929 0 +Sample Unassigned_MappingQuality Unassigned_Nonjunction Unassigned_Unmapped Unassigned_Chimera percent_assigned Unassigned_NoFeatures Unassigned_Secondary Assigned Unassigned_FragmentLength Unassigned_Duplicate Unassigned_MultiMapping Unassigned_Ambiguity Total +70: TopHat on data 1, data 4, and data 3: accepted_hits 0 0 0 0 70.82267755353567 111117 0 321797 0 0 19123 2333 454370 +75: TopHat on data 1, data 6, and data 5: accepted_hits 0 0 0 0 69.58585803304067 165786 0 445012 0 0 25293 3424 639515 +80: TopHat on data 1, data 8, and data 7: accepted_hits 0 0 0 0 71.76957768385707 129664 0 394981 0 0 22580 3121 550346 +85: TopHat on data 1, data 10, and data 9: accepted_hits 0 0 0 0 72.02454351337069 146327 0 437485 0 0 19907 3692 607411 +90: TopHat on data 1, data 12, and data 11: accepted_hits 0 0 0 0 71.33130826437625 132063 0 388170 0 0 21164 2782 544179 +95: TopHat on data 1, data 14, and data 13: accepted_hits 0 0 0 0 70.72517103678439 160805 0 453929 0 0 23533 3554 641821 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/flexbar_stats.tabular --- a/test-data/flexbar_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/flexbar_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample processed_bases discarded_reads_overall finally_skipped_short_reads skipped_due_to_uncalled_bases removed_bases remaining_bases remaining_reads short_prior_to_adapter_removal removed_bases_pct processed_reads -result_right 422 3 3 0 191 231 10 0 45.26066350710901 13 +Sample remaining_reads removed_bases finally_skipped_short_reads skipped_due_to_uncalled_bases short_prior_to_adapter_removal processed_reads processed_bases removed_bases_pct discarded_reads_overall remaining_bases +result_right 10 191 3 0 0 13 422 45.26066350710901 3 231 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/gatk_varianteval_stats.tabular --- a/test-data/gatk_varianteval_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/gatk_varianteval_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample nocalls mnps novel_titv mixed deletions snps known_titv titv_reference complex symbolic insertions -varianteval_1_gatk_varianteval 1330372586 0 2.2 0 0 19199310 0.0 none 0 0 0 +Sample mnps symbolic complex nocalls deletions known_titv titv_reference novel_titv snps mixed insertions +gatk_varianteval 0 0 0 1330372586 0 0.0 none 2.2 19199310 0 0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/hisat2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ -Sample overall_alignment_rate unpaired_aligned_multi unpaired_aligned_none unpaired_total unpaired_aligned_one -hisat2_1 96.15 9953 3849 99978 86176 -hisat2_2 96.15 9953 3849 99978 86176 +Sample unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none unpaired_total unpaired_aligned_one +hisat2_1 9953 96.15 3849 99978 86176 +hisat2_2 9953 96.15 3849 99978 86176 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/htseq_stats.tabular --- a/test-data/htseq_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/htseq_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample alignment_not_unique percent_assigned total_count assigned not_aligned no_feature ambiguous too_low_aQual -htseq 0 0.0 1355 0 1336 19 0 0 +Sample alignment_not_unique assigned total_count not_aligned percent_assigned no_feature too_low_aQual ambiguous +htseq 0 0 1355 1336 0.0 19 0 0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/kallisto_stats.tabular --- a/test-data/kallisto_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/kallisto_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,3 +1,3 @@ -Sample fragment_length percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.6511456908 58016047.0 9484959.0 48531088.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.5027847355 70152623.0 10871703.0 59280920.0 +Sample pseudoaligned_reads not_pseudoaligned_reads total_reads percent_aligned fragment_length +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 9484959.0 58016047.0 83.65114569077758 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 10871703.0 70152623.0 84.50278473550448 169.418 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_AlignmentSummaryMetrics_stats.tabular --- a/test-data/picard_AlignmentSummaryMetrics_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_AlignmentSummaryMetrics_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample PF_HQ_ALIGNED_READS READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH BAD_CYCLES PF_INDEL_RATE PCT_READS_ALIGNED_IN_PAIRS TOTAL_READS PCT_CHIMERAS PF_HQ_ERROR_RATE PF_ALIGNED_BASES PCT_PF_READS LIBRARY PF_READS PCT_ADAPTER PCT_PF_READS_ALIGNED READ_GROUP SAMPLE PF_NOISE_READS STRAND_BALANCE PF_HQ_ALIGNED_Q20_BASES CATEGORY PF_HQ_MEDIAN_MISMATCHES PF_HQ_ALIGNED_BASES PF_MISMATCH_RATE PF_READS_ALIGNED -D11_H4K16ac_Rep1_R1_fastq_gz 11288718.0 0.0 74.733459 0.0 0.000848 0.0 16199126.0 0.0 0.006165 1189439864.0 1.0 16199126.0 1.4e-05 0.983085 112.0 0.494061 802235299.0 UNPAIRED 0.0 843872901.0 0.011597 15925118.0 +Sample CATEGORY PF_HQ_ALIGNED_Q20_BASES PF_HQ_ALIGNED_BASES READ_GROUP PF_HQ_ALIGNED_READS PF_MISMATCH_RATE LIBRARY PCT_READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH PF_HQ_MEDIAN_MISMATCHES SAMPLE PF_HQ_ERROR_RATE READS_ALIGNED_IN_PAIRS PF_READS TOTAL_READS PF_INDEL_RATE PCT_ADAPTER STRAND_BALANCE PCT_PF_READS PF_READS_ALIGNED PF_NOISE_READS BAD_CYCLES PCT_CHIMERAS PF_ALIGNED_BASES PCT_PF_READS_ALIGNED +D11_H4K16ac_Rep1_R1_fastq_gz UNPAIRED 802235299.0 843872901.0 11288718.0 0.011597 0.0 74.733459 0.0 0.006165 0.0 16199126.0 16199126.0 0.000848 1.4e-05 0.494061 1.0 15925118.0 112.0 0.0 0.0 1189439864.0 0.983085 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_RnaSeqMetrics_stats.tabular --- a/test-data/picard_RnaSeqMetrics_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_RnaSeqMetrics_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample PCT_CODING_BASES RIBOSOMAL_BASES PF_NOT_ALIGNED_BASES PCT_MRNA_BASES CORRECT_STRAND_READS MEDIAN_CV_COVERAGE PCT_RIBOSOMAL_BASES PCT_INTRONIC_BASES MEDIAN_3PRIME_BIAS PF_ALIGNED_BASES LIBRARY MEDIAN_5PRIME_BIAS PCT_USABLE_BASES PF_BASES READ_GROUP IGNORED_READS SAMPLE INTERGENIC_BASES INTRONIC_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_INTERGENIC_BASES PCT_CORRECT_STRAND_READS INCORRECT_STRAND_READS CODING_BASES UTR_BASES PCT_UTR_BASES -picard_CollectRnaSeqMetrics_bam 0.0 158.0 79.6231 0.0 0.91593 0.0 0.235755 48712.0 0.430026 79.3657 48870.0 0.0 9926.0 0.0 1.402829 20.3769 0.0 0.0 0.0 38786.0 79.6231 +Sample READ_GROUP INCORRECT_STRAND_READS PF_NOT_ALIGNED_BASES PCT_CODING_BASES PCT_USABLE_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_CORRECT_STRAND_READS RIBOSOMAL_BASES LIBRARY IGNORED_READS PCT_INTRONIC_BASES INTRONIC_BASES PCT_INTERGENIC_BASES PCT_RIBOSOMAL_BASES MEDIAN_3PRIME_BIAS SAMPLE MEDIAN_CV_COVERAGE UTR_BASES INTERGENIC_BASES CORRECT_STRAND_READS PCT_UTR_BASES CODING_BASES MEDIAN_5PRIME_BIAS PCT_MRNA_BASES PF_BASES PF_ALIGNED_BASES +picard_CollectRnaSeqMetrics_bam 0.0 158.0 0.0 79.36569999999999 1.402829 0.0 0.0 0.0 0.0 20.3769 0.235755 0.91593 38786.0 9926.0 0.0 79.62310000000001 0.0 0.430026 79.62310000000001 48870.0 48712.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_baseContent_stats.tabular --- a/test-data/picard_baseContent_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_baseContent_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample mean_pct_a mean_pct_g sum_pct_g mean_pct_t sum_pct_a mean_pct_c sum_pct_t sum_pct_c sum_pct_n cycle_count -D11_H4K16ac_Rep1_R1_fastq_gz 30.02120486666666 21.205210626666666 1590.390797 28.154420613333333 2251.5903649999996 20.61250701333334 2111.581546 1545.9380260000005 0.49925800000000015 75 +Sample mean_pct_t mean_pct_g sum_pct_c sum_pct_t mean_pct_c mean_pct_a sum_pct_n cycle_count sum_pct_g sum_pct_a +D11_H4K16ac_Rep1_R1_fastq_gz 28.154420613333333 21.205210626666666 1545.9380260000005 2111.581546 20.61250701333334 30.02120486666666 0.49925800000000015 75 1590.390797 2251.5903649999996 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_dups_stats.tabular --- a/test-data/picard_dups_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_dups_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample LIBRARY UNPAIRED_READS_EXAMINED ESTIMATED_LIBRARY_SIZE READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION UNMAPPED_READS READ_PAIRS_EXAMINED -dataset_114 Unknown Library 2900.0 77973949.0 629.0 2257.0 0.0 0.005582 0.0 313405.0 +Sample READ_PAIR_DUPLICATES UNPAIRED_READS_EXAMINED LIBRARY READ_PAIRS_EXAMINED UNPAIRED_READ_DUPLICATES UNMAPPED_READS ESTIMATED_LIBRARY_SIZE PERCENT_DUPLICATION READ_PAIR_OPTICAL_DUPLICATES +dataset_114 629.0 2900.0 Unknown Library 313405.0 2257.0 0.0 77973949.0 0.005582 0.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/post_aligner_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/post_aligner_soft_report.html Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b'@@ -0,0 +1,7363 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+<!--\n+ __ __ _ _ _ ___ ____\n+ | \\/ |_ _| | |_(_)/ _ \\ / ___|\n+ | |\\/| | | | | | __| | | | | |\n+ | | | | |_| | | |_| | |_| | |___\n+ |_| |_|\\__,_|_|\\__|_|\\__\\_\\\\____|\n+\n+Abandon hope all ye who enter here..\n+http://multiqc.info\n+-->\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+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\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+\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 467486f1c568 -r e0f4a651c6b9 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/post_aligner_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,21 +1,22 @@ -Sample QUAST_N50-2-1 QUAST_Total_length-2-1 featureCounts_Assigned-1 featureCounts_percent_assigned-1-1 Picard_PCT_PF_READS_ALIGNED-1 Prokka_contigs-1 Prokka_bases-1 Prokka_CDS-1 Prokka_organism-1 Bcftools Stats_number_of_SNPs-1 Bcftools Stats_tstv-1 Bcftools Stats_number_of_records-1 Bcftools Stats_number_of_MNPs-1 Bcftools Stats_number_of_indels-1 Bamtools_duplicates_pct-1-1 Bamtools_mapped_reads_pct-1-1 Picard_PERCENT_DUPLICATION-1 Picard_summed_mean-1 Picard_summed_median-1 HTSeq Count_percent_assigned-2 HTSeq Count_assigned-1 Picard_PCT_RIBOSOMAL_BASES-1 Picard_PCT_MRNA_BASES-1 Samtools Flagstat_mapped_passed-1-1 Samtools Stats_reads_mapped_percent-1 Samtools Stats_raw_total_sequences-1-1 Samtools Stats_reads_mapped-1 Samtools Stats_error_rate-1 Samtools Stats_non_primary_alignments-1 GATK VariantEval_known_titv-1 GATK VariantEval_novel_titv-1 Samblaster_pct_dups-1 -14892_1#15 115136.0 18435361.0 -70: TopHat on data 1, data 4, and data 3: accepted_hits 321797 70.82267755353567 -75: TopHat on data 1, data 6, and data 5: accepted_hits 445012 69.58585803304067 -80: TopHat on data 1, data 8, and data 7: accepted_hits 394981 71.76957768385707 -85: TopHat on data 1, data 10, and data 9: accepted_hits 437485 72.02454351337069 -90: TopHat on data 1, data 12, and data 11: accepted_hits 388170 71.33130826437625 -95: TopHat on data 1, data 14, and data 13: accepted_hits 453929 70.72517103678439 -D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 -Sample1 30 1629978 1548 Helicobacter pylori -Sample2 52 162997532523 1548 Escherichia coli -Test1 4474244.0 1.97 5522770.0 72330.0 902934.0 -bamtools 0.0 93.125 -dataset_114 0.005582 -dataset_197 271.809759 176 -htseq 0.0 0 -picard_CollectRnaSeqMetrics_bam 79.62310000000001 -samtools_flagstat 20689039 -samtools_stats 100.0 641821.0 641821.0 0.004248509 12111.0 -varianteval_1_gatk_varianteval 0.0 2.2 -virtual-normal 1.28 +Sample QUAST_mqc-generalstats-N50 QUAST_mqc-generalstats-Total_length featureCounts_mqc-generalstats-percent_assigned featureCounts_mqc-generalstats-Assigned Picard_mqc-generalstats-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-contigs Prokka_mqc-generalstats-organism Prokka_mqc-generalstats-bases Prokka_mqc-generalstats-CDS Bcftools Stats_mqc-generalstats-tstv Bcftools Stats_mqc-generalstats-number_of_MNPs Bcftools Stats_mqc-generalstats-number_of_indels Bcftools Stats_mqc-generalstats-number_of_SNPs Bcftools Stats_mqc-generalstats-number_of_records Bamtools_mqc-generalstats-duplicates_pct Bamtools_mqc-generalstats-mapped_reads_pct Picard_mqc-generalstats-PERCENT_DUPLICATION Picard_mqc-generalstats-summed_median Picard_mqc-generalstats-summed_mean GATK VariantEval_mqc-generalstats-known_titv GATK VariantEval_mqc-generalstats-novel_titv HTSeq Count_mqc-generalstats-percent_assigned HTSeq Count_mqc-generalstats-assigned Picard_mqc-generalstats-PCT_MRNA_BASES Picard_mqc-generalstats-PCT_RIBOSOMAL_BASES Samtools Flagstat_mqc-generalstats-mapped_passed Samtools Stats_mqc-generalstats-raw_total_sequences Samtools Stats_mqc-generalstats-non_primary_alignments Samtools Stats_mqc-generalstats-reads_mapped Samtools Stats_mqc-generalstats-error_rate Samtools Stats_mqc-generalstats-reads_mapped_percent SnpEff_mqc-generalstats-Ts_Tv_ratio SnpEff_mqc-generalstats-Number_of_variants_before_filter SnpEff_mqc-generalstats-Change_rate Samblaster_mqc-generalstats-pct_dups +14892_1#15 115136.0 18435361.0 +70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 +75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 +80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 +85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 +90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 +95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 +D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 +Sample1 30 Helicobacter pylori 1629978 1548 +Sample2 52 Escherichia coli 162997532523 1548 +Test1 1.97 72330.0 902934.0 4474244.0 5522770.0 +bamtools 0.0 93.125 +dataset_114 0.005582 +dataset_197 176 271.809759 +gatk_varianteval 0.0 2.2 +htseq 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat 20689039 +samtools_stats 641821.0 12111.0 641821.0 0.004248509 100.0 +snpeff 0.0 972155.0 3190.0 +virtual-normal 1.28 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_log.txt --- a/test-data/pre_alignment_soft_log.txt Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/pre_alignment_soft_log.txt Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b"@@ -1,75 +1,85 @@\n-[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc2/lib/python2.7/site-packages/multiqc-1.2-py2.7.egg/multiqc_config.yaml\n-[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml\n-[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml\n-[2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir\n-[2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2\n-[2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2\n-[2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir\n-[2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc\n-[2017-09-28 17:24:02,210] multiqc [INFO ] Template : default\n-[2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir'\n-[2017-09-28 17:24:02,211] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rseqc, busco, goleft_indexcov, disambiguate, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bismark, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq\n-[2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig\n-[2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found\n-[2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50\n-[2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n-[2017-09-28 17:24:05,430] multiqc.modules.busco.busco "..b"orts\n+[2018-04-05 12:06:48,307] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs\n+[2018-04-05 12:06:48,318] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs\n+[2018-04-05 12:06:48,325] multiqc [DEBUG ] No samples found: skewer\n+[2018-04-05 12:06:48,334] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs\n+[2018-04-05 12:06:48,339] multiqc [DEBUG ] No samples found: biobloomtools\n+[2018-04-05 12:06:48,346] multiqc [DEBUG ] No samples found: fastq_screen\n+[2018-04-05 12:06:48,352] multiqc [DEBUG ] No samples found: afterqc\n+[2018-04-05 12:06:48,434] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports\n+[2018-04-05 12:06:48,495] multiqc [DEBUG ] No samples found: clusterflow\n+[2018-04-05 12:06:48,500] multiqc [DEBUG ] No samples found: bcl2fastq\n+[2018-04-05 12:06:48,505] multiqc [DEBUG ] No samples found: interop\n+[2018-04-05 12:06:48,514] multiqc [INFO ] Compressing plot data\n+[2018-04-05 12:06:48,596] multiqc [INFO ] Report : multiqc_report.html\n+[2018-04-05 12:06:48,597] multiqc [INFO ] Data : multiqc_data\n+[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_data.json' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,599] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'\n+[2018-04-05 12:06:48,809] multiqc [INFO ] MultiQC complete\n" |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pre_alignment_soft_report.html Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b'@@ -0,0 +1,5990 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+<!--\n+ __ __ _ _ _ ___ ____\n+ | \\/ |_ _| | |_(_)/ _ \\ / ___|\n+ | |\\/| | | | | | __| | | | | |\n+ | | | | |_| | | |_| | |_| | |___\n+ |_| |_|\\__,_|_|\\__|_|\\__\\_\\\\____|\n+\n+Abandon hope all ye who enter here..\n+http://multiqc.info\n+-->\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+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\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+\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' |
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| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/pre_alignment_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
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| @@ -1,7 +1,7 @@ -Sample SortMeRNA_rRNA_pct-1 Trimmomatic_dropped_pct-1 Cutadapt_percent_trimmed-1 FastQC_percent_gc-1 FastQC_total_sequences-1 FastQC_avg_sequence_length-1 FastQC_percent_duplicates-1 FastQC_percent_fails-1 Flexbar_removed_bases_pct-1 +Sample SortMeRNA_mqc-generalstats-rRNA_pct Trimmomatic_mqc-generalstats-dropped_pct Cutadapt_mqc-generalstats-percent_trimmed FastQC_mqc-generalstats-avg_sequence_length FastQC_mqc-generalstats-percent_fails FastQC_mqc-generalstats-percent_duplicates FastQC_mqc-generalstats-percent_gc FastQC_mqc-generalstats-total_sequences Flexbar_mqc-generalstats-removed_bases_pct 25839_merged 1.099299750020029 C2 17.98 dataset_33 10.776820436239396 -poulet5_1 48.0 267849.0 101.0 36.30591159931017 8.333333333333332 -poulet5_2 48.0 267849.0 101.0 36.173388748054116 8.333333333333332 +poulet5_1 101.0 8.333333333333332 36.30591159931017 48.0 267849.0 +poulet5_2 101.0 8.333333333333332 36.173388748054116 48.0 267849.0 result_right 45.26066350710901 |
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| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/prokka_stats.tabular --- a/test-data/prokka_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/prokka_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
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| @@ -1,3 +1,3 @@ -Sample tRNA CDS rRNA repeat_region bases organism contigs sig_peptide tmRNA misc_RNA -Sample1 36 1548 2 15 1629978 Helicobacter pylori 30 88 1 -Sample2 1548 2 162997532523 Escherichia coli 52 5152 +Sample repeat_region sig_peptide bases organism tmRNA contigs tRNA rRNA CDS misc_RNA +Sample1 15 88 1629978 Helicobacter pylori 1 30 36 2 1548 +Sample2 162997532523 Escherichia coli 52 2 1548 5152 |
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| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/quast_stats.tabular --- a/test-data/quast_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/quast_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample # mismatches per 100 kbp # misassembled contigs Largest contig # indels per 100 kbp LG75 # local misassemblies Total length (>= 25000 bp) Total length N50 NGA50 Reference GC (%) # contigs (>= 10000 bp) LA75 NG50 # genes_partial # unaligned contigs Total length (>= 50000 bp) LA50 # contigs (>= 25000 bp) NA75 GC (%) LG50 NA50 LGA75 # contigs (>= 0 bp) Largest alignment Total length (>= 0 bp) # genes # misassemblies NGA75 Total length (>= 10000 bp) # contigs (>= 5000 bp) L75 Total length (>= 1000 bp) # unaligned contigs_partial # contigs (>= 50000 bp) Total length (>= 5000 bp) N75 # contigs (>= 1000 bp) LGA50 Duplication ratio Genome fraction (%) NG75 Unaligned length # N's per 100 kbp Misassembled contigs length Reference length L50 # contigs -14892_1#15 262.21 82.0 435484.0 33.75 106.0 132.0 17353907.0 18435361.0 115136.0 99244.0 48.21 215.0 117.0 112874.0 968.0 8.0 15112131.0 56.0 181.0 54365.0 48.17 50.0 102129.0 124.0 545.0 356982.0 18465341.0 7280.0 107.0 51757.0 17893099.0 242.0 100.0 18373173.0 59.0 123.0 18079934.0 62262.0 376.0 59.0 1.016 95.482 56990.0 88446.0 929.55 4540800.0 18916112.0 48.0 467.0 +Sample LG50 # contigs # misassemblies # local misassemblies # misassembled contigs NA50 # genes # indels per 100 kbp Reference length # contigs (>= 10000 bp) Total length (>= 1000 bp) GC (%) Reference GC (%) Unaligned length Misassembled contigs length Genome fraction (%) Largest alignment L75 NG75 # contigs (>= 1000 bp) Largest contig N75 NGA50 NA75 LA50 LGA75 Total length LG75 Total length (>= 50000 bp) # contigs (>= 50000 bp) # mismatches per 100 kbp Total length (>= 25000 bp) Total length (>= 10000 bp) Total length (>= 5000 bp) Total length (>= 0 bp) # unaligned contigs_partial # contigs (>= 25000 bp) LA75 # contigs (>= 0 bp) N50 LGA50 # genes_partial NGA75 # contigs (>= 5000 bp) Duplication ratio NG50 # unaligned contigs # N's per 100 kbp L50 +14892_1#15 50.0 467.0 107.0 132.0 82.0 102129.0 7280.0 33.75 18916112.0 215.0 18373173.0 48.17 48.21 88446.0 4540800.0 95.482 356982.0 100.0 56990.0 376.0 435484.0 62262.0 99244.0 54365.0 56.0 124.0 18435361.0 106.0 15112131.0 123.0 262.21 17353907.0 17893099.0 18079934.0 18465341.0 59.0 181.0 117.0 545.0 115136.0 59.0 968.0 51757.0 242.0 1.016 112874.0 8.0 929.55 48.0 |
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| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/report_manual_custom_content.html --- a/test-data/report_manual_custom_content.html Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/report_manual_custom_content.html Fri Apr 20 01:06:25 2018 -0400 |
| [ |
| b'@@ -0,0 +1,4823 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+<!--\n+ __ __ _ _ _ ___ ____\n+ | \\/ |_ _| | |_(_)/ _ \\ / ___|\n+ | |\\/| | | | | | __| | | | | |\n+ | | | | |_| | | |_| | |_| | |___\n+ |_| |_|\\__,_|_|\\__|_|\\__\\_\\\\____|\n+\n+Abandon hope all ye who enter here..\n+http://multiqc.info\n+-->\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+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\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+\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 467486f1c568 -r e0f4a651c6b9 test-data/salmon.txt --- a/test-data/salmon.txt Sun Jan 14 09:55:46 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2 +0,0 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|
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/salmon_flenDist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_flenDist.txt Fri Apr 20 01:06:25 2018 -0400 |
| b |
| b'@@ -0,0 +1,2 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|
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/salmon_meta_info.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_meta_info.json Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +{ + "salmon_version": "0.6.0", + "samp_type": "none", + "frag_dist_length": 2001, + "bias_correct": true, + "num_bias_bins": 4096, + "mapping_type": "mapping", + "num_targets": 209539, + "num_bootstraps": 0, + "num_processed": 439147, + "num_mapped": 367866, + "percent_mapped": 83.76830537382699, + "call": "quant", + "start_time": "Thu Mar 31 13:09:43 2016" +} \ No newline at end of file |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samblaster_stats.tabular --- a/test-data/samblaster_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samblaster_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample n_dups pct_dups n_tot n_nondups -virtual-normal 1 1.28 78 77 +Sample n_nondups n_tot n_dups pct_dups +virtual-normal 77 78 1 1.28 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samtools_flagstat_stats.tabular --- a/test-data/samtools_flagstat_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samtools_flagstat_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample mapped_passed duplicates_failed secondary_passed paired in sequencing_failed duplicates_passed read2_passed read1_failed read1_passed with mate mapped to a different chr_passed total_failed properly paired_passed_pct singletons_passed supplementary_passed singletons_passed_pct mapped_failed_pct mapped_passed_pct supplementary_failed with itself and mate mapped_failed mapped_failed total_passed properly paired_failed flagstat_total with mate mapped to a different chr (mapQ >= 5)_passed properly paired_failed_pct with mate mapped to a different chr (mapQ >= 5)_failed with itself and mate mapped_passed read2_failed with mate mapped to a different chr_failed properly paired_passed paired in sequencing_passed singletons_failed secondary_failed singletons_failed_pct -samtools_flagstat 20689039 0 0 0 5448463 0 0 0 0 0 nan 0 0 nan nan 98.33 0 0 0 21040602 0 21040602 0 nan 0 0 0 0 0 0 0 0 nan +Sample read2_passed mapped_failed_pct with mate mapped to a different chr (mapQ >= 5)_passed properly paired_passed read1_passed total_passed supplementary_failed duplicates_failed singletons_failed mapped_passed_pct secondary_passed properly paired_passed_pct properly paired_failed_pct singletons_passed with mate mapped to a different chr (mapQ >= 5)_failed supplementary_passed duplicates_passed flagstat_total mapped_passed with mate mapped to a different chr_failed secondary_failed properly paired_failed with itself and mate mapped_failed with mate mapped to a different chr_passed paired in sequencing_failed with itself and mate mapped_passed singletons_passed_pct total_failed paired in sequencing_passed read1_failed mapped_failed read2_failed singletons_failed_pct +samtools_flagstat 0 nan 0 0 0 21040602 0 0 0 98.33 0 nan nan 0 0 0 5448463 21040602 20689039 0 0 0 0 0 0 0 nan 0 0 0 0 0 nan |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samtools_stats_stats.tabular --- a/test-data/samtools_stats_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samtools_stats_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample insert_size_average reads_mapped_and_paired reads_QC_failed_percent outward_oriented_pairs 1st_fragments bases_duplicated reads_MQ0 bases_mapped maximum_length bases_trimmed reads_duplicated inward_oriented_pairs sequences error_rate insert_size_standard_deviation non-primary_alignments reads_unmapped_percent mismatches reads_mapped_and_paired_percent reads_mapped_percent raw_total_sequences reads_mapped pairs_on_different_chromosomes reads_MQ0_percent pairs_with_other_orientation reads_paired_percent total_length reads_unmapped average_length reads_duplicated_percent bases_mapped_(cigar) average_quality reads_properly_paired reads_properly_paired_percent reads_QC_failed last_fragments filtered_sequences reads_paired is_sorted -samtools_stats 719.7 638746.0 0.0 1294.0 320981.0 0.0 70.0 64823921.0 101.0 0.0 0.0 317512.0 641821.0 0.004248509 1223.0 12111.0 0.0 275405.0 99.52089445499603 100.0 641821.0 641821.0 0.0 0.010906467691147531 30.0 100.0 64823921.0 0.0 101.0 0.0 64823921.0 26.0 635626.0 99.03477760933345 0.0 320840.0 0.0 641821.0 1.0 +Sample is_sorted insert_size_standard_deviation reads_paired_percent reads_QC_failed bases_mapped 1st_fragments reads_mapped_and_paired_percent error_rate mismatches reads_properly_paired bases_mapped_(cigar) reads_MQ0 reads_duplicated reads_duplicated_percent inward_oriented_pairs sequences non-primary_alignments reads_MQ0_percent reads_mapped_percent reads_mapped_and_paired average_length last_fragments average_quality outward_oriented_pairs total_length bases_duplicated raw_total_sequences bases_trimmed pairs_on_different_chromosomes reads_properly_paired_percent reads_mapped reads_unmapped_percent maximum_length reads_paired reads_QC_failed_percent insert_size_average reads_unmapped filtered_sequences pairs_with_other_orientation +samtools_stats 1.0 1223.0 100.0 0.0 64823921.0 320981.0 99.52089445499603 0.004248509 275405.0 635626.0 64823921.0 70.0 0.0 0.0 317512.0 641821.0 12111.0 0.010906467691147531 100.0 638746.0 101.0 320840.0 26.0 1294.0 64823921.0 0.0 641821.0 0.0 0.0 99.03477760933345 641821.0 0.0 101.0 641821.0 0.0 719.7 0.0 0.0 30.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/snpeff_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+Sample\tMODERATE\tsplice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant_percent\tsplice_region_variant+non_coding_exon_variant\tframeshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent\tframeshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant\tsplice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant\tframeshift_variant+start_lost+splice_region_variant_percent\tNONE\tintragenic_variant_percent\tsplice_region_variant+non_coding_exon_variant_percent\tUTR_3_PRIME\tsplice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant\tTs_Tv_ratio\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tinframe_insertion+splice_region_variant_percent\tUTR_3_PRIME_percent\tinframe_deletion+splice_region_variant\t5_prime_UTR_truncation+exon_loss_variant\tdisruptive_inframe_deletion_percent\tINTRON\tLOW\tHet\tstart_lost+disruptive_inframe_insertion\tframeshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant_percent\tinframe_deletion\tsplice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent\tnon_coding_exon_variant\tframeshift_variant+stop_gained\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tDOWNSTREAM_percent\tdisruptive_inframe_deletion+splice_region_variant\tMOTIF\tframeshift_variant+start_lost+splice_region_variant\tsplice_donor_variant+splice_region_variant+splice_region_variant+intron_variant\tframeshift_variant+stop_gained_percent\tEXON\tsplice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant\tupstream_gene_variant\tintron_variant_percent\tsplice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent\tinframe_deletion_percent\tHIGH_percent\t3_prime_UTR_variant\tsplice_donor_variant+intron_variant\tframeshift_variant+start_lost_percent\tdisruptive_inframe_insertion\tnon_coding_exon_variant_percent\tChange_rate\t5_prime_UTR_truncation+exon_loss_variant_percent\tMODERATE_percent\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent\tUTR_5_PRIME\tTRANSCRIPT\tframeshift_variant\tdownstream_gene_variant\tMODIFIER_percent\tsplice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent\tLOW_percent\tframeshift_variant+splice_region_variant\tMissense_Silent_ratio\tMissing\tdisruptive_inframe_deletion+splice_region_variant_percent\tsplice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent\tframeshift_variant+stop_lost\tframeshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant\tsequence_feature_percent\tintron_variant\tframeshift_variant+splice_region_variant_percent\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant\tsplice_donor_variant+5_prime_UTR_variant+intron_variant\tNumber_of_known_variants <br>(i.e. non-empty ID)_percent\tstart_lost+disruptive_inframe_insertion_percent\tsplice_acceptor_variant+splice_donor_variant+intron_variant\tTransitions\tDOWNSTREAM\tSPLICE_SITE_DONOR_percent\tframeshift_variant+stop_lost_percent\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent\tsplice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tEXON_percent\tframeshift_variant_percent\tNumber_of_variants_before_filter\tdisruptive_inframe_insertion_percent\tsplice_acceptor_variant+splice'..b'ence_feature\tintergenic_region_percent\ttranscript_percent\tHIGH\tframeshift_variant+splice_donor_variant+splice_region_variant+intron_variant\tUPSTREAM\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tinframe_deletion+splice_region_variant_percent\ttranscript\tsplice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tGenome_total_length\tNumber_of_effects\tNONE_percent\tframeshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant\tSPLICE_SITE_ACCEPTOR_percent\tsplice_acceptor_variant+intron_variant_percent\tsplice_donor_variant+intron_variant_percent\tsplice_donor_variant+5_prime_UTR_variant+intron_variant_percent\tsplice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent\tsplice_acceptor_variant+splice_donor_variant+intron_variant_percent\tsplice_donor_variant+splice_region_variant+intron_variant\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent\tTransversions\tGenome\tdisruptive_inframe_deletion\tMODIFIER\tsplice_acceptor_variant+splice_region_variant+intron_variant_percent\tframeshift_variant+start_lost\tSPLICE_SITE_REGION_percent\tsplice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant\tINTRON_percent\tsplice_acceptor_variant+5_prime_UTR_variant+intron_variant_percent\tsplice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant\tTF_binding_site_variant\tMOTIF_percent\tframeshift_variant+splice_donor_variant+splice_region_variant+intron_variant_percent\tinframe_insertion\tsplice_region_variant+intron_variant\tstop_gained+inframe_insertion_percent\tinframe_insertion+splice_region_variant\tNumber_of_known_variants <br>(i.e. non-empty ID)\tsplice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant\t3_prime_UTR_variant_percent\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant\tsplice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent\tdownstream_gene_variant_percent\tINTERGENIC\tsplice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant\tsplice_region_variant+splice_region_variant\tsplice_donor_variant+splice_region_variant+intron_variant_percent\tsplice_region_variant\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant\tsplice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant\tsplice_region_variant+intron_variant_percent\tsplice_region_variant_percent\tSPLICE_SITE_DONOR\tinframe_insertion_percent\tintergenic_region\tTRANSCRIPT_percent\tintragenic_variant\n+snpeff\t3322.0\t1.8e-05\t462.0\t0.000109\t1.0\t1.0\t1.8e-05\t2174772.0\t0.004855\t0.0084\t15811.0\t1.8e-05\t2.0\t0.0\t9.1e-05\t3.6e-05\t0.287478\t10.0\t2.0\t0.007418\t2126738.0\t2178258.0\t524875.0\t1.0\t1.8e-05\t159.0\t0.000127\t15320.0\t21.0\t3.6e-05\t6.178119\t2.0\t986.0\t1.0\t3.0\t0.000382\t17369.0\t1.0\t354347.0\t38.668709\t1.8e-05\t0.002891\t0.024855\t15811.0\t41.0\t0.000145\t277.0\t0.278551\t3190.0\t3.6e-05\t0.060401\t1.8e-05\t3352.0\t1.0\t800.0\t339790.0\t60.30929\t1.8e-05\t39.605454\t77.0\t?\t0.0\t3.6e-05\t1.8e-05\t3.0\t2.0\t39.535817\t2126738.0\t0.0014\t13.0\t2.0\t78.616167\t1.8e-05\t61.0\t0.0\t339790.0\t0.001473\t5.5e-05\t3.6e-05\t9.1e-05\t0.315806\t0.014546\t972155.0\t0.005036\t5.5e-05\t224.0\t3.0\t6.442797\t360.0\t0.017928\t5040.0\t3101536026.0\t3.6e-05\t2.0\t8.386471\t5.0\t3350.0\t6.442797\t12.0\t1.0\t32.0\t0.06091\tCount\t1.0\t392480.0\t1.0\t1.8e-05\t0.060947\t2174428.0\t8.386471\t0.0014\t1367.0\t3.0\t354347.0\t0.000236\t0.000182\t77.0\t9.1e-05\t32036512383.0\t5499894.0\t39.542071\t6.0\t0.006546\t0.004073\t0.000745\t3.6e-05\t0.000218\t0.001109\t15.0\t1.8e-05\t0.0\tGRCh37.75\t408.0\t3316947.0\t0.000582\t8.0\t0.091638\t5.0\t38.668709\t3.6e-05\t7.0\t986.0\t0.017928\t5.5e-05\t266.0\t4390.0\t5.5e-05\t2.0\t764271.0\t5.0\t0.287478\t1.0\t5.5e-05\t6.178119\t461247.0\t2.0\t1.0\t0.000273\t187.0\t3.0\t1.0\t0.07982\t0.0034\t81.0\t0.004836\t461247.0\t1.8e-05\t267.0\n' |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/sortmerna_stats.tabular --- a/test-data/sortmerna_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/sortmerna_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample non_rRNA silva-euk-18s-id95_count silva-euk-18s-id95_pct rRNA_pct silva-arc-16s-id95_count silva-euk-28s-id98_pct rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_count rfam-5s-database-id98_count silva-bac-23s-id98_count silva-bac-23s-id98_pct rfam-5.8s-database-id98_count silva-arc-16s-id95_pct non_rRNA_pct rfam-5s-database-id98_pct silva-arc-23s-id98_count silva-arc-23s-id98_pct total silva-bac-16s-id90_pct silva-euk-28s-id98_count -25839_merged 4394708 11108.89 0.25 1.099299750020029 0.0 0.01 0.0 48848 26216.9804 0.0 10664.534399999999 0.24 0.0 0.0 98.90070024997996 0.0 0.0 0.0 4443556 0.59 444.35560000000004 +Sample silva-euk-28s-id98_count silva-arc-16s-id95_count silva-euk-18s-id95_pct silva-bac-23s-id98_pct silva-arc-23s-id98_pct rfam-5s-database-id98_count rRNA_pct silva-bac-16s-id90_count rfam-5.8s-database-id98_count silva-euk-18s-id95_count rRNA silva-euk-28s-id98_pct silva-arc-16s-id95_pct total rfam-5s-database-id98_pct non_rRNA_pct rfam-5.8s-database-id98_pct silva-bac-23s-id98_count silva-arc-23s-id98_count silva-bac-16s-id90_pct non_rRNA +25839_merged 444.35560000000004 0.0 0.25 0.24 0.0 0.0 1.099299750020029 26216.9804 0.0 11108.89 48848 0.01 0.0 4443556 0.0 98.90070024997996 0.0 10664.534399999999 0.0 0.59 4394708 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/star_stats.tabular --- a/test-data/star_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/star_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample unmapped_tooshort multimapped mismatch_rate num_splices total_reads num_GCAG_splices unmapped_mismatches_percent avg_mapped_read_length num_GTAG_splices deletion_length avg_input_read_length multimapped_percent deletion_rate uniquely_mapped unmapped_tooshort_percent unmapped_mismatches unmapped_other_percent insertion_length multimapped_toomany_percent num_noncanonical_splices unmapped_other multimapped_toomany insertion_rate num_annotated_splices uniquely_mapped_percent num_ATAC_splices -star_log 10 1.0 1.73 47.0 100.0 0.0 0.0 74.8 47.0 0.0 75.0 1.0 0.0 89.0 10.0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0.0 89.0 0.0 +Sample multimapped_percent insertion_rate multimapped_toomany_percent num_annotated_splices num_GTAG_splices uniquely_mapped unmapped_tooshort_percent deletion_length mismatch_rate insertion_length num_noncanonical_splices num_ATAC_splices deletion_rate multimapped_toomany total_reads num_GCAG_splices num_splices unmapped_mismatches_percent unmapped_other_percent unmapped_mismatches unmapped_tooshort multimapped unmapped_other avg_mapped_read_length uniquely_mapped_percent avg_input_read_length +star_log 1.0 0.0 0.0 0.0 47.0 89.0 10.0 0.0 1.73 0.0 0.0 0.0 0.0 0.0 100.0 0.0 47.0 0.0 0.0 0 10 1.0 0 74.8 89.0 75.0 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/tophat_stats.tabular --- a/test-data/tophat_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/tophat_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample unaligned_total aligned_total aligned_not_multimapped_discordant overall_aligned_percent aligned_multimap aligned_discordant total_reads concordant_aligned_percent -tophat_align 2985.0 313405.0 307733.0 99.5 5638.0 34.0 316390.0 99.0 +Sample aligned_not_multimapped_discordant concordant_aligned_percent unaligned_total aligned_total aligned_multimap total_reads aligned_discordant overall_aligned_percent +tophat_align 307733.0 99.0 2985.0 313405.0 5638.0 316390.0 34.0 99.5 |
| b |
| diff -r 467486f1c568 -r e0f4a651c6b9 test-data/trimmomatic_stats.tabular --- a/test-data/trimmomatic_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/trimmomatic_stats.tabular Fri Apr 20 01:06:25 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ -Sample input_reads surviving_pct dropped surviving dropped_pct -C2 39733090.0 82.02 7142532.0 32590558.0 17.98 +Sample input_reads surviving dropped surviving_pct dropped_pct +C2 39733090.0 32590558.0 7142532.0 82.02 17.98 |