| Previous changeset 11:f0ec41881020 (2018-08-06) Next changeset 13:161f4383df15 (2019-01-20) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 |
|
modified:
multiqc.xml test-data/aligner_soft_stats.tabular test-data/post_aligner_soft_stats.tabular test-data/pre_alignment_soft_stats.tabular |
|
added:
test-data/fastp1.json.txt test-data/fastp2.json.txt test-data/fastp_stats.tabular |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 multiqc.xml --- a/multiqc.xml Mon Aug 06 10:42:11 2018 -0400 +++ b/multiqc.xml Wed Aug 08 08:49:39 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> - <token name="@WRAPPER_VERSION@">1.5</token> + <token name="@WRAPPER_VERSION@">1.6</token> <token name="@ESCAPE_IDENTIFIER@"> <![CDATA[ #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) @@ -156,6 +156,14 @@ @LN_2_FILES@ #end if #end for + #elif str($repeat.software_cond.software) == "fastp" + #set $pattern = "report_title" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json') + ln -s '$file' '$file_path' && + grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" && + #end for #elif str($repeat.software_cond.software) == "fastqc" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) @CREATE_REPEAT_DIR_1@ @@ -499,6 +507,7 @@ <option value="deeptools">deepTools</option> <!--<option value="disambiguate">Disambiguate</option>--> <!--<option value="fastq_screen">FastQ Screen</option>--> + <option value="fastp">fastp</option> <option value="fastqc">FastQC</option> <option value="featureCounts">featureCounts</option> <option value="flexbar">Flexbar</option> @@ -584,6 +593,9 @@ <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> </repeat> </when> + <when value="fastp"> + <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/> + </when> <when value="fastqc"> <repeat name="output" title="FastQC output" min="1"> <param name="type" type="select" label="Type of FastQC output?"> @@ -813,6 +825,12 @@ </repeat> <repeat name="results"> <conditional name="software_cond"> + <param name="software" value="fastp" /> + <param name="input" value="fastp1.json.txt,fastp2.json.txt" /> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> <param name="software" value="fastqc" /> <repeat name="output"> <param name="type" value="data"/> @@ -846,6 +864,7 @@ <has_text text="Title of the report" /> <has_text text="Commment for the report" /> <has_text text="cutadapt_plot" /> + <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> <has_text text="fastqc_seq_heatmap_key_t" /> <has_text text="flexbar_plot" /> <has_text text="sortmerna-detailed-plot" /> @@ -855,6 +874,7 @@ <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/> <output_collection name="stats" type="list"> <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> + <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/aligner_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-percent_aligned Kallisto_mqc-generalstats-pseudoaligned_reads Bismark_mqc-generalstats-aligned_reads Bismark_mqc-generalstats-percent_aligned Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Pairs_considered HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Min_rest_site_distance 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 MACS2_mqc-generalstats-d MACS2_mqc-generalstats-treatment_redundant_rate MACS2_mqc-generalstats-control_redundant_rate +Sample Cutadapt_mqc-generalstats-cutadapt-percent_trimmed Kallisto_mqc-generalstats-kallisto-fragment_length Kallisto_mqc-generalstats-kallisto-percent_aligned Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads Bismark_mqc-generalstats-bismark-aligned_reads Bismark_mqc-generalstats-bismark-percent_aligned Bowtie 2_mqc-generalstats-bowtie_2-overall_alignment_rate HiCExplorer_mqc-generalstats-hicexplorer-Pairs_considered HiCExplorer_mqc-generalstats-hicexplorer-Pairs_used HiCExplorer_mqc-generalstats-hicexplorer-Mapped HiCExplorer_mqc-generalstats-hicexplorer-Min_rest_site_distance HiCExplorer_mqc-generalstats-hicexplorer-Max_rest_site_distance HISAT2_mqc-generalstats-hisat2-overall_alignment_rate STAR_mqc-generalstats-star-uniquely_mapped_percent STAR_mqc-generalstats-star-uniquely_mapped Tophat_mqc-generalstats-tophat-overall_aligned_percent Tophat_mqc-generalstats-tophat-aligned_not_multimapped_discordant MACS2_mqc-generalstats-macs2-d MACS2_mqc-generalstats-macs2-treatment_redundant_rate MACS2_mqc-generalstats-macs2-control_redundant_rate HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/fastp1.json.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp1.json.txt Wed Aug 08 08:49:39 2018 -0400 |
| [ |
| b'@@ -0,0 +1,217 @@\n+{\n+\t"summary": {\n+\t\t"before_filtering": {\n+\t\t\t"total_reads":2,\n+\t\t\t"total_bases":302,\n+\t\t\t"q20_bases":262,\n+\t\t\t"q30_bases":241,\n+\t\t\t"q20_rate":0.86755,\n+\t\t\t"q30_rate":0.798013,\n+\t\t\t"read1_mean_length":151,\n+\t\t\t"gc_content":0.36755\n+\t\t},\n+\t\t"after_filtering": {\n+\t\t\t"total_reads":2,\n+\t\t\t"total_bases":286,\n+\t\t\t"q20_bases":246,\n+\t\t\t"q30_bases":226,\n+\t\t\t"q20_rate":0.86014,\n+\t\t\t"q30_rate":0.79021,\n+\t\t\t"read1_mean_length":143,\n+\t\t\t"gc_content":0.367133\n+\t\t}\n+\t},\n+\t"filtering_result": {\n+\t\t"passed_filter_reads": 2,\n+\t\t"low_quality_reads": 0,\n+\t\t"too_many_N_reads": 0,\n+\t\t"too_short_reads": 0,\n+\t\t"too_long_reads": 0\n+\t},\n+\t"duplication": {\n+\t\t"rate": 0,\n+\t\t"histogram": [2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],\n+\t\t"mean_gc": [0.407843,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]\n+\t},\n+\t"read1_before_filtering": {\n+\t\t"total_reads": 2,\n+\t\t"total_bases": 302,\n+\t\t"q20_bases": 262,\n+\t\t"q30_bases": 241,\n+\t\t"total_cycles": 151,\n+\t\t"quality_curves": {\n+\t\t\t"A":[26.5,32,32,32,32,36,36,36,36,36,21,25,36,23,34,32,25,36,14,34,36,26.5,21,36,36,14,14,36,36,36,21,28.5,36,34,36,36,36,36,36,36,36,25,36,25,25,36,25,34,36,36,36,36,36,25,32,25,34,36,36,25,36,36,32,36,36,36,36,34,36,36,36,36,36,28.5,36,36,36,36,32,14,36,25,34,25,28.5,36,25,28.5,14,36,28.5,36,36,36,36,36,21,36,25,36,34,34,34,25,36,32,25,36,36,36,36,36,36,25,31.5,36,36,36,34,36,36,25,34,25,36,36,27,32,36,36,36,34,36,36,36,23,36,32,31.5,36,36,20.5,34,34,36,36,14,36,36,36,25],\n+\t\t\t"T":[26.5,32,32,32,32,34,36,36,36,36,28.5,25,36,32,36,32,25,36,25,34,36,26.5,28.5,36,36,25,36,34,36,36,28.5,28.5,25,34,34,36,25,25,36,36,36,25,36,36,36,36,25,36,34,25,36,36,36,25,36,25,32,36,36,25,36,36,32,25,25,36,36,32,36,36,36,36,36,28.5,36,36,32,32,34,25,36,25,34,25,28.5,36,25,28.5,14,25,36,27,36,34,34,36,28.5,36,36,31.5,32,36,36,25,36,32,25,36,36,36,36,36,36,36,31.5,27,36,36,34,36,25,25,34,25,36,36,29.5,29.5,36,25,34,34,36,14,27,23,34,36,31.5,14,36,20.5,34,34,32,36,23,34,27,36,25],\n+\t\t\t"C":[26.5,32,32,32,32,34,36,36,36,36,28.5,36,36,23,32,32,25,36,25,34,36,26.5,28.5,36,36,25,25,34,36,36,28.5,28.5,14,32,32,36,14,14,36,36,36,14,36,25,25,36,25,32,32,14,36,36,36,25,34,25,34,36,36,25,36,36,32,25,25,36,36,34,36,36,36,36,36,28.5,36,36,34,34,34,36,36,14,32,14,28.5,36,25,21,14,25,21,31.5,36,32,32,36,28.5,36,14,27,34,34,34,25,36,32,25,36,36,36,36,36,36,14,31.5,31.5,36,36,34,36,25,25,34,25,36,36,32,27,36,25,32,34,36,25,31.5,23,32,34,31.5,25,36,20.5,34,34,34,36,23,34,31.5,36,25],\n+\t\t\t"G":[26.5,32,32,32,32,32,36,36,36,36,36,14,36,14,34,32,25,36,36,34,36,26.5,36,36,36,36,25,32,36,36,36,28.5,25,36,34,36,25,25,36,36,36,36,36,14,14,36,25,34,34,25,36,36,36,25,34,25,36,36,36,25,36,36,32,14,14,36,36,36,36,36,36,36,36,28.5,36,36,34,34,36,25,36,36,36,36,28.5,36,25,36,14,14,28.5,31.5,36,34,34,36,36,36,25,31.5,36,32,32,25,36,32,25,36,36,36,36,36,36,25,31.5,31.5,36,36,34,36,14,25,34,25,36,36,29.5,29.5,36,14,34,34,36,25,31.5,23,34,34,31.5,25,36,20.5,34,34,34,36,32,32,31.5,36,25],\n+\t\t\t"mean":[26.5,32,32,32,32,34,36,36,36,36,28.5,25,36,23,34,32,25,36,25,34,36,26.5,28.5,36,36,25,25,34,36,36,28.5,28.5,25,34,34,36,25,25,36,36,36,25,36,25,25,36,25,34,34,25,36,36,36,25,34,25,34,36,36,25,36,36,32,25,25,36,36,34,36,36,36,36,36,28.5,36,36,34,34,34,25,36,25,34,25,28.5,36,25,28.5,14,25,28.5,31.5,36,34,34,36,28.5,36,25,31.5,34,34,34,25,36,32,25,36,36,36,36,36,36,25,31.5,31.5,36,36,34,36,25,25,34,25,36,36,29.5,29.5,36,25,34,34,36,25,31.5,23,34,34,31.5,25,36,20.5,34,34,34,36,23,34,31.5,36,25]\n+\t\t},\n+\t\t"content_curves": {\n+\t\t\t"A":[0,1,0,0.5,1,0.5,0.5,0,0,0,0.5,0,1,0,0,0.5,0,0,0.5,1,0.5,1,0.5,0,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0,0.5,0,0.5,0.5,0.5,0.5,0.5,0,0,0,0,0,0,0,1,0,0.5,0.5,1,0.5,0.5,0,0.5,0,0,0.5,0.5,1,0.5,0,0.5,0.5,0.5,0,0.5,0,0,0,1,1,1,0,0.5,0,0.5,0.5,0.5,0.5,0.5,0,0,0,1,0.5,0,0,0.5,0.5,0,0.5,0.5,0.5,0.5,0.5,0.5,0,0,0.5,0,0,0,1,0,1,0,0,0.5,0,0.5,1,0,0,1,0.5,0.5,0.5,1,1,0.5,0,0,0,0.5,1,0.5,0.5,0,0.5,0.5,1,1,0.5,0.5,0,0.5,0.5,0,0.5,0.5,1,0,1,0.5,0.5,0.5,0.5,0.5,0.5,0],\n+\t\t\t"T":[1,0,0,0,0,0,0,0.5,0'..b'\n+\t\t\t"CGCAA":0,\t\t\t"CGCAT":0,\t\t\t"CGCAC":0,\t\t\t"CGCAG":0,\t\t\t"CGCTA":0,\t\t\t"CGCTT":1,\t\t\t"CGCTC":0,\t\t\t"CGCTG":1,\t\t\t"CGCCA":0,\t\t\t"CGCCT":0,\t\t\t"CGCCC":0,\t\t\t"CGCCG":0,\t\t\t"CGCGA":0,\t\t\t"CGCGT":0,\t\t\t"CGCGC":0,\t\t\t"CGCGG":0,\n+\t\t\t"CGGAA":0,\t\t\t"CGGAT":0,\t\t\t"CGGAC":0,\t\t\t"CGGAG":0,\t\t\t"CGGTA":0,\t\t\t"CGGTT":0,\t\t\t"CGGTC":0,\t\t\t"CGGTG":0,\t\t\t"CGGCA":0,\t\t\t"CGGCT":0,\t\t\t"CGGCC":0,\t\t\t"CGGCG":0,\t\t\t"CGGGA":1,\t\t\t"CGGGT":0,\t\t\t"CGGGC":0,\t\t\t"CGGGG":0,\n+\t\t\t"GAAAA":1,\t\t\t"GAAAT":2,\t\t\t"GAAAC":0,\t\t\t"GAAAG":1,\t\t\t"GAATA":1,\t\t\t"GAATT":0,\t\t\t"GAATC":0,\t\t\t"GAATG":0,\t\t\t"GAACA":0,\t\t\t"GAACT":0,\t\t\t"GAACC":1,\t\t\t"GAACG":0,\t\t\t"GAAGA":0,\t\t\t"GAAGT":0,\t\t\t"GAAGC":0,\t\t\t"GAAGG":1,\n+\t\t\t"GATAA":0,\t\t\t"GATAT":0,\t\t\t"GATAC":0,\t\t\t"GATAG":0,\t\t\t"GATTA":0,\t\t\t"GATTT":0,\t\t\t"GATTC":0,\t\t\t"GATTG":0,\t\t\t"GATCA":0,\t\t\t"GATCT":0,\t\t\t"GATCC":0,\t\t\t"GATCG":0,\t\t\t"GATGA":0,\t\t\t"GATGT":0,\t\t\t"GATGC":0,\t\t\t"GATGG":0,\n+\t\t\t"GACAA":0,\t\t\t"GACAT":2,\t\t\t"GACAC":0,\t\t\t"GACAG":0,\t\t\t"GACTA":0,\t\t\t"GACTT":0,\t\t\t"GACTC":0,\t\t\t"GACTG":0,\t\t\t"GACCA":0,\t\t\t"GACCT":0,\t\t\t"GACCC":0,\t\t\t"GACCG":0,\t\t\t"GACGA":0,\t\t\t"GACGT":0,\t\t\t"GACGC":0,\t\t\t"GACGG":0,\n+\t\t\t"GAGAA":1,\t\t\t"GAGAT":0,\t\t\t"GAGAC":0,\t\t\t"GAGAG":1,\t\t\t"GAGTA":1,\t\t\t"GAGTT":0,\t\t\t"GAGTC":0,\t\t\t"GAGTG":0,\t\t\t"GAGCA":1,\t\t\t"GAGCT":0,\t\t\t"GAGCC":1,\t\t\t"GAGCG":0,\t\t\t"GAGGA":0,\t\t\t"GAGGT":1,\t\t\t"GAGGC":0,\t\t\t"GAGGG":0,\n+\t\t\t"GTAAA":3,\t\t\t"GTAAT":0,\t\t\t"GTAAC":0,\t\t\t"GTAAG":0,\t\t\t"GTATA":1,\t\t\t"GTATT":0,\t\t\t"GTATC":0,\t\t\t"GTATG":0,\t\t\t"GTACA":1,\t\t\t"GTACT":0,\t\t\t"GTACC":2,\t\t\t"GTACG":0,\t\t\t"GTAGA":0,\t\t\t"GTAGT":0,\t\t\t"GTAGC":0,\t\t\t"GTAGG":0,\n+\t\t\t"GTTAA":0,\t\t\t"GTTAT":0,\t\t\t"GTTAC":0,\t\t\t"GTTAG":0,\t\t\t"GTTTA":0,\t\t\t"GTTTT":0,\t\t\t"GTTTC":0,\t\t\t"GTTTG":0,\t\t\t"GTTCA":0,\t\t\t"GTTCT":0,\t\t\t"GTTCC":0,\t\t\t"GTTCG":0,\t\t\t"GTTGA":0,\t\t\t"GTTGT":0,\t\t\t"GTTGC":0,\t\t\t"GTTGG":0,\n+\t\t\t"GTCAA":0,\t\t\t"GTCAT":0,\t\t\t"GTCAC":0,\t\t\t"GTCAG":0,\t\t\t"GTCTA":0,\t\t\t"GTCTT":0,\t\t\t"GTCTC":0,\t\t\t"GTCTG":0,\t\t\t"GTCCA":0,\t\t\t"GTCCT":0,\t\t\t"GTCCC":0,\t\t\t"GTCCG":0,\t\t\t"GTCGA":0,\t\t\t"GTCGT":0,\t\t\t"GTCGC":0,\t\t\t"GTCGG":1,\n+\t\t\t"GTGAA":0,\t\t\t"GTGAT":0,\t\t\t"GTGAC":1,\t\t\t"GTGAG":1,\t\t\t"GTGTA":0,\t\t\t"GTGTT":0,\t\t\t"GTGTC":0,\t\t\t"GTGTG":0,\t\t\t"GTGCA":0,\t\t\t"GTGCT":0,\t\t\t"GTGCC":0,\t\t\t"GTGCG":0,\t\t\t"GTGGA":0,\t\t\t"GTGGT":1,\t\t\t"GTGGC":0,\t\t\t"GTGGG":0,\n+\t\t\t"GCAAA":1,\t\t\t"GCAAT":0,\t\t\t"GCAAC":0,\t\t\t"GCAAG":0,\t\t\t"GCATA":0,\t\t\t"GCATT":0,\t\t\t"GCATC":1,\t\t\t"GCATG":0,\t\t\t"GCACA":1,\t\t\t"GCACT":0,\t\t\t"GCACC":0,\t\t\t"GCACG":0,\t\t\t"GCAGA":0,\t\t\t"GCAGT":1,\t\t\t"GCAGC":1,\t\t\t"GCAGG":0,\n+\t\t\t"GCTAA":0,\t\t\t"GCTAT":0,\t\t\t"GCTAC":0,\t\t\t"GCTAG":0,\t\t\t"GCTTA":0,\t\t\t"GCTTT":1,\t\t\t"GCTTC":1,\t\t\t"GCTTG":0,\t\t\t"GCTCA":0,\t\t\t"GCTCT":0,\t\t\t"GCTCC":0,\t\t\t"GCTCG":0,\t\t\t"GCTGA":1,\t\t\t"GCTGT":0,\t\t\t"GCTGC":0,\t\t\t"GCTGG":1,\n+\t\t\t"GCCAA":0,\t\t\t"GCCAT":0,\t\t\t"GCCAC":0,\t\t\t"GCCAG":0,\t\t\t"GCCTA":0,\t\t\t"GCCTT":0,\t\t\t"GCCTC":0,\t\t\t"GCCTG":0,\t\t\t"GCCCA":1,\t\t\t"GCCCT":0,\t\t\t"GCCCC":0,\t\t\t"GCCCG":0,\t\t\t"GCCGA":0,\t\t\t"GCCGT":0,\t\t\t"GCCGC":0,\t\t\t"GCCGG":0,\n+\t\t\t"GCGAA":0,\t\t\t"GCGAT":0,\t\t\t"GCGAC":0,\t\t\t"GCGAG":0,\t\t\t"GCGTA":0,\t\t\t"GCGTT":0,\t\t\t"GCGTC":0,\t\t\t"GCGTG":0,\t\t\t"GCGCA":0,\t\t\t"GCGCT":0,\t\t\t"GCGCC":0,\t\t\t"GCGCG":0,\t\t\t"GCGGA":0,\t\t\t"GCGGT":0,\t\t\t"GCGGC":0,\t\t\t"GCGGG":0,\n+\t\t\t"GGAAA":1,\t\t\t"GGAAT":1,\t\t\t"GGAAC":1,\t\t\t"GGAAG":1,\t\t\t"GGATA":0,\t\t\t"GGATT":1,\t\t\t"GGATC":0,\t\t\t"GGATG":0,\t\t\t"GGACA":0,\t\t\t"GGACT":0,\t\t\t"GGACC":0,\t\t\t"GGACG":0,\t\t\t"GGAGA":1,\t\t\t"GGAGT":1,\t\t\t"GGAGC":1,\t\t\t"GGAGG":1,\n+\t\t\t"GGTAA":2,\t\t\t"GGTAT":1,\t\t\t"GGTAC":1,\t\t\t"GGTAG":0,\t\t\t"GGTTA":0,\t\t\t"GGTTT":0,\t\t\t"GGTTC":0,\t\t\t"GGTTG":0,\t\t\t"GGTCA":0,\t\t\t"GGTCT":0,\t\t\t"GGTCC":0,\t\t\t"GGTCG":1,\t\t\t"GGTGA":0,\t\t\t"GGTGT":0,\t\t\t"GGTGC":0,\t\t\t"GGTGG":0,\n+\t\t\t"GGCAA":0,\t\t\t"GGCAT":0,\t\t\t"GGCAC":0,\t\t\t"GGCAG":2,\t\t\t"GGCTA":0,\t\t\t"GGCTT":0,\t\t\t"GGCTC":0,\t\t\t"GGCTG":0,\t\t\t"GGCCA":0,\t\t\t"GGCCT":0,\t\t\t"GGCCC":0,\t\t\t"GGCCG":0,\t\t\t"GGCGA":0,\t\t\t"GGCGT":0,\t\t\t"GGCGC":0,\t\t\t"GGCGG":0,\n+\t\t\t"GGGAA":2,\t\t\t"GGGAT":0,\t\t\t"GGGAC":0,\t\t\t"GGGAG":0,\t\t\t"GGGTA":1,\t\t\t"GGGTT":0,\t\t\t"GGGTC":0,\t\t\t"GGGTG":0,\t\t\t"GGGCA":0,\t\t\t"GGGCT":0,\t\t\t"GGGCC":0,\t\t\t"GGGCG":0,\t\t\t"GGGGA":0,\t\t\t"GGGGT":1,\t\t\t"GGGGC":0,\t\t\t"GGGGG":0\n+\t\t},\n+\t\t"overrepresented_sequences": {\n+\t\t}\n+\t},\n+\t"command": "fastp --thread 1 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 "\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/fastp2.json.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp2.json.txt Wed Aug 08 08:49:39 2018 -0400 |
| [ |
| b'@@ -0,0 +1,412 @@\n+{\n+\t"summary": {\n+\t\t"before_filtering": {\n+\t\t\t"total_reads":198,\n+\t\t\t"total_bases":49698,\n+\t\t\t"q20_bases":45944,\n+\t\t\t"q30_bases":43923,\n+\t\t\t"q20_rate":0.924464,\n+\t\t\t"q30_rate":0.883798,\n+\t\t\t"read1_mean_length":251,\n+\t\t\t"read2_mean_length":251,\n+\t\t\t"gc_content":0.480422\n+\t\t},\n+\t\t"after_filtering": {\n+\t\t\t"total_reads":194,\n+\t\t\t"total_bases":45884,\n+\t\t\t"q20_bases":43215,\n+\t\t\t"q30_bases":41653,\n+\t\t\t"q20_rate":0.941832,\n+\t\t\t"q30_rate":0.907789,\n+\t\t\t"read1_mean_length":236,\n+\t\t\t"read2_mean_length":236,\n+\t\t\t"gc_content":0.479928\n+\t\t}\n+\t},\n+\t"filtering_result": {\n+\t\t"passed_filter_reads": 194,\n+\t\t"low_quality_reads": 2,\n+\t\t"too_many_N_reads": 2,\n+\t\t"too_short_reads": 0,\n+\t\t"too_long_reads": 0\n+\t},\n+\t"duplication": {\n+\t\t"rate": 0,\n+\t\t"histogram": [69,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],\n+\t\t"mean_gc": [0.396022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]\n+\t},\n+\t"insert_size": {\n+\t\t"peak": 308,\n+\t\t"unknown": 4,\n+\t\t"histogram": [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,1,0,1,1,1,1,0,0,0,1,0,2,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0,0,2,0,0,0,1,0,2,0,1,0,1,3,1,0,0,0,0,0,0,1,0,1,0,2,0,0,1,1,0,1,0,0,1,0,1,1,1,1,0,1,1,0,2,1,1,0,1,0,1,1,0,1,0,0,0,2,0,0,0,2,1,1,2,1,0,0,1,1,2,0,0,2,1,0,0,2,0,1,0,0,1,2,0,4,2,0,0,0,1,0,1,1,0,0,0,0,0,0,0,0,1,1,0,0,1,0,1,0,2,1,1,1,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]\n+\t},\n+\t"adapter_cutting": {\n+\t\t"adapter_trimmed_reads": 66,\n+\t\t"adapter_trimmed_bases": 2810,\n+\t\t"read1_adapter_sequence": "unspecified",\n+\t\t"read2_adapter_sequence": "unspecified",\n+\t\t"read1_adapter_counts": {"CTG":2, "CTGTC":1, "CTGTCTCTTATACA":1, "CTGTCTCTTATACAC":3, "CTGTCTCTTATACACA":1, "CTGTCTATTATACACATC":1, "CTGTCTCTTATACACATCTC":1, "CTGTCTCTTATACACCTCTC":1, "CTGTCTCTTATACACATCTCCG":1, "CTGTCTCTTATACACATCTCCGAGCC":2, "CTGTCTCTTATACACATCTCCGAGCCCACGAG":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATTTCGT":1, "CTGTCTCTTATACACATATCCACGCCCACGAGACTAAGGCGAAGTTCATT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATG":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGTATGCCGT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCAGTT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGGATGCCGTCT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCT":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGTATGCCGTCTTCTGCTTGA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAAAAAAAAAATAG":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAACAACAGAC":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGACTTCTGCTTGAAAAAAAAAAACTACAACCCACGGACGCA":1, "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGACAAAAAAAAACACACAACAACCAACACCCAGTAGACTAGTGCGTC":1},\n+\t\t"read2_adapter_counts": {"CTG":1, "CTT":1, "CTGTC":1, "CTGTCTCTTATACA":1, "CTGTCTCTTATACAC":3, "CTGTCTCTTATACACA":1, "CTGTCTCTTATACACATT":1, "CTGTCTCTTATACACATCTG":2, "CTGTCTCTTATACACATCTGAC":1, "CTGTCTCTTATACACATCTGAGCTTC":1, "CTGTCTCTTATACACATTTG'..b'":0,\t\t\t"CGCGA":53,\t\t\t"CGCGT":43,\t\t\t"CGCGC":0,\t\t\t"CGCGG":2,\n+\t\t\t"CGGAA":1,\t\t\t"CGGAT":7,\t\t\t"CGGAC":0,\t\t\t"CGGAG":50,\t\t\t"CGGTA":1,\t\t\t"CGGTT":1,\t\t\t"CGGTC":0,\t\t\t"CGGTG":1,\t\t\t"CGGCA":0,\t\t\t"CGGCT":45,\t\t\t"CGGCC":0,\t\t\t"CGGCG":0,\t\t\t"CGGGA":53,\t\t\t"CGGGT":2,\t\t\t"CGGGC":4,\t\t\t"CGGGG":0,\n+\t\t\t"GAAAA":45,\t\t\t"GAAAT":0,\t\t\t"GAAAC":0,\t\t\t"GAAAG":2,\t\t\t"GAATA":1,\t\t\t"GAATT":0,\t\t\t"GAATC":40,\t\t\t"GAATG":1,\t\t\t"GAACA":7,\t\t\t"GAACT":16,\t\t\t"GAACC":9,\t\t\t"GAACG":59,\t\t\t"GAAGA":0,\t\t\t"GAAGT":9,\t\t\t"GAAGC":0,\t\t\t"GAAGG":0,\n+\t\t\t"GATAA":35,\t\t\t"GATAT":1,\t\t\t"GATAC":49,\t\t\t"GATAG":94,\t\t\t"GATTA":0,\t\t\t"GATTT":0,\t\t\t"GATTC":39,\t\t\t"GATTG":0,\t\t\t"GATCA":52,\t\t\t"GATCT":0,\t\t\t"GATCC":41,\t\t\t"GATCG":1,\t\t\t"GATGA":40,\t\t\t"GATGT":42,\t\t\t"GATGC":1,\t\t\t"GATGG":51,\n+\t\t\t"GACAA":0,\t\t\t"GACAT":119,\t\t\t"GACAC":1,\t\t\t"GACAG":45,\t\t\t"GACTA":0,\t\t\t"GACTT":1,\t\t\t"GACTC":0,\t\t\t"GACTG":1,\t\t\t"GACCA":1,\t\t\t"GACCT":44,\t\t\t"GACCC":10,\t\t\t"GACCG":0,\t\t\t"GACGA":44,\t\t\t"GACGT":0,\t\t\t"GACGC":53,\t\t\t"GACGG":0,\n+\t\t\t"GAGAA":0,\t\t\t"GAGAT":0,\t\t\t"GAGAC":53,\t\t\t"GAGAG":45,\t\t\t"GAGTA":1,\t\t\t"GAGTT":0,\t\t\t"GAGTC":0,\t\t\t"GAGTG":42,\t\t\t"GAGCA":50,\t\t\t"GAGCT":96,\t\t\t"GAGCC":52,\t\t\t"GAGCG":0,\t\t\t"GAGGA":0,\t\t\t"GAGGT":1,\t\t\t"GAGGC":39,\t\t\t"GAGGG":1,\n+\t\t\t"GTAAA":0,\t\t\t"GTAAT":36,\t\t\t"GTAAC":1,\t\t\t"GTAAG":28,\t\t\t"GTATA":0,\t\t\t"GTATT":52,\t\t\t"GTATC":72,\t\t\t"GTATG":27,\t\t\t"GTACA":0,\t\t\t"GTACT":0,\t\t\t"GTACC":0,\t\t\t"GTACG":0,\t\t\t"GTAGA":0,\t\t\t"GTAGT":0,\t\t\t"GTAGC":12,\t\t\t"GTAGG":48,\n+\t\t\t"GTTAA":51,\t\t\t"GTTAT":3,\t\t\t"GTTAC":0,\t\t\t"GTTAG":2,\t\t\t"GTTTA":1,\t\t\t"GTTTT":18,\t\t\t"GTTTC":0,\t\t\t"GTTTG":0,\t\t\t"GTTCA":19,\t\t\t"GTTCT":0,\t\t\t"GTTCC":78,\t\t\t"GTTCG":29,\t\t\t"GTTGA":1,\t\t\t"GTTGT":0,\t\t\t"GTTGC":0,\t\t\t"GTTGG":1,\n+\t\t\t"GTCAA":0,\t\t\t"GTCAT":39,\t\t\t"GTCAC":0,\t\t\t"GTCAG":0,\t\t\t"GTCTA":52,\t\t\t"GTCTT":80,\t\t\t"GTCTC":45,\t\t\t"GTCTG":52,\t\t\t"GTCCA":0,\t\t\t"GTCCT":11,\t\t\t"GTCCC":0,\t\t\t"GTCCG":0,\t\t\t"GTCGA":0,\t\t\t"GTCGT":0,\t\t\t"GTCGC":50,\t\t\t"GTCGG":7,\n+\t\t\t"GTGAA":15,\t\t\t"GTGAT":113,\t\t\t"GTGAC":1,\t\t\t"GTGAG":43,\t\t\t"GTGTA":0,\t\t\t"GTGTT":8,\t\t\t"GTGTC":0,\t\t\t"GTGTG":77,\t\t\t"GTGCA":94,\t\t\t"GTGCT":44,\t\t\t"GTGCC":0,\t\t\t"GTGCG":37,\t\t\t"GTGGA":2,\t\t\t"GTGGT":41,\t\t\t"GTGGC":1,\t\t\t"GTGGG":22,\n+\t\t\t"GCAAA":0,\t\t\t"GCAAT":45,\t\t\t"GCAAC":1,\t\t\t"GCAAG":0,\t\t\t"GCATA":0,\t\t\t"GCATT":120,\t\t\t"GCATC":0,\t\t\t"GCATG":45,\t\t\t"GCACA":43,\t\t\t"GCACT":0,\t\t\t"GCACC":77,\t\t\t"GCACG":51,\t\t\t"GCAGA":0,\t\t\t"GCAGT":49,\t\t\t"GCAGC":0,\t\t\t"GCAGG":40,\n+\t\t\t"GCTAA":14,\t\t\t"GCTAT":63,\t\t\t"GCTAC":0,\t\t\t"GCTAG":1,\t\t\t"GCTTA":1,\t\t\t"GCTTT":0,\t\t\t"GCTTC":0,\t\t\t"GCTTG":5,\t\t\t"GCTCA":0,\t\t\t"GCTCT":54,\t\t\t"GCTCC":138,\t\t\t"GCTCG":0,\t\t\t"GCTGA":1,\t\t\t"GCTGT":0,\t\t\t"GCTGC":1,\t\t\t"GCTGG":51,\n+\t\t\t"GCCAA":0,\t\t\t"GCCAT":0,\t\t\t"GCCAC":0,\t\t\t"GCCAG":0,\t\t\t"GCCTA":1,\t\t\t"GCCTT":0,\t\t\t"GCCTC":34,\t\t\t"GCCTG":29,\t\t\t"GCCCA":50,\t\t\t"GCCCT":0,\t\t\t"GCCCC":0,\t\t\t"GCCCG":0,\t\t\t"GCCGA":1,\t\t\t"GCCGT":0,\t\t\t"GCCGC":0,\t\t\t"GCCGG":52,\n+\t\t\t"GCGAA":6,\t\t\t"GCGAT":88,\t\t\t"GCGAC":45,\t\t\t"GCGAG":53,\t\t\t"GCGTA":0,\t\t\t"GCGTT":0,\t\t\t"GCGTC":45,\t\t\t"GCGTG":44,\t\t\t"GCGCA":1,\t\t\t"GCGCT":0,\t\t\t"GCGCC":0,\t\t\t"GCGCG":0,\t\t\t"GCGGA":0,\t\t\t"GCGGT":1,\t\t\t"GCGGC":0,\t\t\t"GCGGG":1,\n+\t\t\t"GGAAA":2,\t\t\t"GGAAT":39,\t\t\t"GGAAC":34,\t\t\t"GGAAG":0,\t\t\t"GGATA":16,\t\t\t"GGATT":0,\t\t\t"GGATC":52,\t\t\t"GGATG":40,\t\t\t"GGACA":2,\t\t\t"GGACT":1,\t\t\t"GGACC":0,\t\t\t"GGACG":0,\t\t\t"GGAGA":44,\t\t\t"GGAGT":2,\t\t\t"GGAGC":153,\t\t\t"GGAGG":0,\n+\t\t\t"GGTAA":3,\t\t\t"GGTAT":53,\t\t\t"GGTAC":0,\t\t\t"GGTAG":11,\t\t\t"GGTTA":43,\t\t\t"GGTTT":20,\t\t\t"GGTTC":33,\t\t\t"GGTTG":1,\t\t\t"GGTCA":38,\t\t\t"GGTCT":52,\t\t\t"GGTCC":0,\t\t\t"GGTCG":1,\t\t\t"GGTGA":33,\t\t\t"GGTGT":53,\t\t\t"GGTGC":80,\t\t\t"GGTGG":2,\n+\t\t\t"GGCAA":0,\t\t\t"GGCAT":0,\t\t\t"GGCAC":1,\t\t\t"GGCAG":40,\t\t\t"GGCTA":19,\t\t\t"GGCTT":1,\t\t\t"GGCTC":48,\t\t\t"GGCTG":0,\t\t\t"GGCCA":0,\t\t\t"GGCCT":0,\t\t\t"GGCCC":4,\t\t\t"GGCCG":0,\t\t\t"GGCGA":7,\t\t\t"GGCGT":0,\t\t\t"GGCGC":0,\t\t\t"GGCGG":0,\n+\t\t\t"GGGAA":24,\t\t\t"GGGAT":12,\t\t\t"GGGAC":0,\t\t\t"GGGAG":53,\t\t\t"GGGTA":13,\t\t\t"GGGTT":3,\t\t\t"GGGTC":38,\t\t\t"GGGTG":131,\t\t\t"GGGCA":1,\t\t\t"GGGCT":22,\t\t\t"GGGCC":3,\t\t\t"GGGCG":0,\t\t\t"GGGGA":35,\t\t\t"GGGGT":64,\t\t\t"GGGGC":2,\t\t\t"GGGGG":126\n+\t\t},\n+\t\t"overrepresented_sequences": {\n+\t\t}\n+\t},\n+\t"command": "fastp --thread 1 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq.fastq -O second.fastq "\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/fastp_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp_stats.tabular Wed Aug 08 08:49:39 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Sample command +R1_fq fastp --thread 1 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 +bwa-mem-fastq1_fq fastp --thread 1 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq.fastq -O second.fastq |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/post_aligner_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 |
| b |
| @@ -1,22 +1,22 @@ -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 +Sample QUAST_mqc-generalstats-quast-N50 QUAST_mqc-generalstats-quast-Total_length featureCounts_mqc-generalstats-featurecounts-percent_assigned featureCounts_mqc-generalstats-featurecounts-Assigned Picard_mqc-generalstats-picard-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-prokka-organism Prokka_mqc-generalstats-prokka-contigs Prokka_mqc-generalstats-prokka-bases Prokka_mqc-generalstats-prokka-CDS Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_records Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_SNPs Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_indels Bcftools Stats_mqc-generalstats-bcftools_stats-tstv Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_MNPs Bamtools_mqc-generalstats-bamtools-duplicates_pct Bamtools_mqc-generalstats-bamtools-mapped_reads_pct Picard_mqc-generalstats-picard-PERCENT_DUPLICATION Picard_mqc-generalstats-picard-summed_median Picard_mqc-generalstats-picard-summed_mean GATK VariantEval_mqc-generalstats-gatk_varianteval-known_titv GATK VariantEval_mqc-generalstats-gatk_varianteval-novel_titv HTSeq Count_mqc-generalstats-htseq_count-percent_assigned HTSeq Count_mqc-generalstats-htseq_count-assigned Picard_mqc-generalstats-picard-PCT_RIBOSOMAL_BASES Picard_mqc-generalstats-picard-PCT_MRNA_BASES Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed Samtools Stats_mqc-generalstats-samtools_stats-error_rate Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences SnpEff_mqc-generalstats-snpeff-Change_rate SnpEff_mqc-generalstats-snpeff-Ts_Tv_ratio SnpEff_mqc-generalstats-snpeff-Number_of_variants_before_filter Samblaster_mqc-generalstats-samblaster-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 Helicobacter pylori 30 1629978 1548 +Sample2 Escherichia coli 52 162997532523 1548 +Test1 5522770.0 4474244.0 902934.0 1.97 72330.0 +bamtools_txt 0.0 93.125 +dataset_114 0.005582 +dataset_197 176 271.809759 +gatk_varianteval_txt 0.0 2.2 +htseq_txt 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat_txt 20689039 +samtools_stats_txt 0.004248509 12111.0 641821.0 100.0 99.03477760933345 0.010906467691147531 641821.0 +snpeff_csv 3190.0 0.0 972155.0 +virtual-normal 1.28 |
| b |
| diff -r f0ec41881020 -r 1c2db0054039 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/pre_alignment_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 |
| b |
| @@ -1,7 +1,9 @@ -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_1 101.0 8.333333333333332 36.30591159931017 48.0 267849.0 -poulet5_2 101.0 8.333333333333332 36.173388748054116 48.0 267849.0 -result_right 45.26066350710901 +Sample SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct fastp_mqc-generalstats-fastp-pct_duplication fastp_mqc-generalstats-fastp-after_filtering_q30_rate fastp_mqc-generalstats-fastp-after_filtering_q30_bases fastp_mqc-generalstats-fastp-after_filtering_gc_content fastp_mqc-generalstats-fastp-pct_surviving fastp_mqc-generalstats-fastp-pct_adapter Cutadapt_mqc-generalstats-cutadapt-percent_trimmed FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences Flexbar_mqc-generalstats-flexbar-removed_bases_pct +25839_merged 1.099299750020029 +C2 17.98 +R1_fq 0.0 0.79021 226.0 0.367133 100.0 +bwa-mem-fastq1_fq 0.0 0.907789 41653.0 0.479928 97.97979797979798 33.33333333333333 +dataset_33 10.776820436239396 +poulet5_1 36.30591159931017 48.0 101.0 8.333333333333332 267849.0 +poulet5_2 36.173388748054116 48.0 101.0 8.333333333333332 267849.0 +result_right 45.26066350710901 |