| Previous changeset 19:f7985e0479b9 (2020-11-21) Next changeset 21:75c93c70d094 (2021-03-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" |
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modified:
multiqc.xml |
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removed:
test-data/aligner_soft_report.html 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/cc_ko15.bpc.embedded.tab test-data/cc_wt15.bpc.embedded.tab test-data/cutadapt_stats.tabular test-data/fastp_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/hicup_deduplicator.txt test-data/hicup_filter.txt test-data/hicup_mapper.txt test-data/hicup_truncater.txt test-data/hisat2_stats.tabular test-data/htseq_stats.tabular test-data/kallisto_stats.tabular test-data/macs_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/picard_insertSize_stats.tabular test-data/post_aligner_soft_report.html test-data/post_aligner_soft_stats.tabular test-data/pre_alignment_soft_report.html test-data/pre_alignment_soft_stats.tabular test-data/prokka_stats.tabular test-data/qualimap_bamqc_genome_results.tabular test-data/quast_stats.tabular test-data/rsem.txt test-data/salmon_flenDist.txt test-data/salmon_meta_info.json test-data/samblaster_stats.tabular test-data/samtools_flagstat_stats.tabular test-data/samtools_stats_stats.tabular test-data/slamdunk_readrates_plus.tabular test-data/snpeff_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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| diff -r f7985e0479b9 -r c1a4b5f3b432 multiqc.xml --- a/multiqc.xml Sat Nov 21 12:54:24 2020 +0000 +++ b/multiqc.xml Tue Mar 02 08:02:36 2021 +0000 |
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| b'@@ -53,6 +53,16 @@\n @CHECK_LN_FILE@\n #end for\n ]]></token>\n+ <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">\n+ <element name="@NAME@">\n+ <assert_contents>\n+ <has_n_columns n="@COLUMNS@"/>\n+ <has_n_lines n="@LINES@"/>\n+ <has_text text="@TEXT@"/>\n+ <yield/>\n+ </assert_contents>\n+ </element>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>\n@@ -339,7 +349,7 @@\n @LN_3_FILES@\n #elif str($repeat2.type.type) == "read_duplication_pos"\n #for $k, $file in enumerate($repeat2.type.input)\n- #set file_path = os.path.join($repeat_dir, \'file_\' + str($k) + \'.pos.DupRate.xls\') \n+ #set file_path = os.path.join($repeat_dir, \'file_\' + str($k) + \'.pos.DupRate.xls\')\n ln -s \'$file\' \'$file_path\' &&\n #end for\n #elif str($repeat2.type.type) == "infer_experiment"\n@@ -931,14 +941,16 @@\n </assert_contents>\n </output>\n <output_collection name="stats" type="list" count="10">\n- <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>\n- <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>\n- <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>\n- <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>\n- <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>\n- <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>\n- <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>\n- <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>\n+ <expand macro="element_assert" name="cutadapt" columns="8" lines="2" text="dataset_33"/>\n+ <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/>\n+ <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/>\n+ <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/>\n+ <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/>\n+ <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>\n+ <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>\n+ <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/>\n+ <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/>\n+ <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/>\n </output_collection>\n <output_collection name="plots" type="list" count="29"/>\n </test>\n@@ -1019,16 +1031,18 @@\n <has_text text="hicexplorer1_log_1" />\n </assert_contents>\n </output>\n- <output_collection name="stats" type="list" count="8">\n- <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>\n- <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>\n- <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>\n- <element name="hisat'..b'ame="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 name="stats" type="list" count="21">\n+ <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/>\n+ <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/>\n+ <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/>\n+ <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/>\n+ <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/>\n+ <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/>\n+ <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/>\n+ <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>\n+ <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/>\n+ <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>\n+ <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/>\n+ <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/>\n+ <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/>\n+ <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/>\n+ <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/>\n+ <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/>\n+ <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt">\n+ <has_text text="samtools_flagstat" />\n+ <has_text text="mapped_passed" />\n+ <has_text text="20689039" />\n+ </expand>\n+ <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/>\n+ <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/>\n+ <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/>\n+ <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/>\n </output_collection>\n </test>\n <test expect_num_outputs="2">\n@@ -1297,8 +1311,12 @@\n <has_text text="fastqc_seq_heatmap_key_t" />\n </assert_contents>\n </output>\n-\t <output_collection name="stats" type="list" count="1"/>\n- <output_collection name="plots" type="list" count="1">\n+\t <output_collection name="stats" type="list" count="3">\n+ <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/>\n+ <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/>\n+ <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/>\n+ </output_collection>\n+ <output_collection name="plots" type="list" count="7">\n <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>\n </output_collection>\n </test>\n' |
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| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/aligner_soft_report.html --- a/test-data/aligner_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,5608 +0,0 @@\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 f7985e0479b9 -r c1a4b5f3b432 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,19 +0,0 @@ -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 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -bismark_txt_SE_report 220558.0 69.71079996207212 -bowtie2_1_txt 98.33 -bowtie2_2_txt 98.31 -hicexplorer_3_hicexplorer1_log_1_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 -hicexplorer_3_hicexplorer1_log_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 -hicexplorer_3_hicexplorer2_log_small_test_rf 99983.0 0.35940109818669175 0.08778492343698428 152.0 1500.0 -hisat2_1_txt 96.15 -hisat2_2_txt 96.15 -star_log_txt 89.0 89.0 -tophat_txtalign 99.5 307733.0 -treat1 254.0 0.0 0.0 -treat2 254.0 0.0 0.0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/bamtools_stats.tabular --- a/test-data/bamtools_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/bcftools_stats.tabular --- a/test-data/bcftools_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/bismark_stats.tabular --- a/test-data/bismark_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 -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 f7985e0479b9 -r c1a4b5f3b432 test-data/bowtie2_stats.tabular --- a/test-data/bowtie2_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Sample unpaired_total total_reads unpaired_aligned_one unpaired_aligned_none overall_alignment_rate unpaired_aligned_multi -bowtie2_1 21040602 21040602 13299463 351563 98.33 7389576 -bowtie2_2 16199126 16199126 10087714 274008 98.31 5837404 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/busco_stats.tabular --- a/test-data/busco_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/cc_ko15.bpc.embedded.tab --- a/test-data/cc_ko15.bpc.embedded.tab Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,1289 +0,0 @@\n-# file_format: 'tsv'\n-# section_name: 'BPC'\n-# title: 'Base peak chromatogram'\n-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'\n-# plot_type: 'linegraph'\n-# pconfig:\n-# id: 'bpc_lineplot'\n-# title: 'Base peak chromatogram'\n-# ylab: 'Base Peak Intensity'\n-# xlab: 'Retention Time'\n-Retention Time\tBase Peak Intensity\n-2502.98928676082\t43888\n-2504.55428676082\t43960\n-2506.11928676082\t43392\n-2507.68428676082\t42632\n-2509.24928676082\t42200\n-2510.81428676082\t42288\n-2512.37928676082\t42664\n-2513.94428676082\t42480\n-2515.50928676082\t42320\n-2517.07428676082\t42528\n-2518.63928676082\t43376\n-2520.20428676082\t44240\n-2521.76928676082\t44696\n-2523.33328676082\t44560\n-2524.89828676082\t44112\n-2526.46328676082\t43936\n-2528.02828676082\t43736\n-2529.59328676082\t42912\n-2531.15828676082\t42360\n-2532.72328676082\t43128\n-2534.28828676082\t43880\n-2535.85328676082\t44104\n-2537.41828676082\t44256\n-2538.98328676082\t44664\n-2540.54828676082\t44600\n-2542.11328676082\t44224\n-2543.67828676082\t44120\n-2545.24328676082\t44328\n-2546.80828676082\t44536\n-2548.37328676082\t44872\n-2549.93828676082\t44592\n-2551.50328676082\t43600\n-2553.06828676082\t42872\n-2554.63328676082\t43528\n-2556.19728676082\t44072\n-2557.76228676082\t43360\n-2559.32728676082\t41632\n-2560.89228676082\t40752\n-2562.45728676082\t40472\n-2564.02228676082\t39792\n-2565.58728676082\t39096\n-2567.15228676082\t39696\n-2568.71728676082\t41152\n-2570.28228676082\t41896\n-2571.84728676082\t41568\n-2573.41228676082\t41448\n-2574.97728676082\t42336\n-2576.54228676082\t43432\n-2578.10728676082\t43720\n-2579.67228676082\t43352\n-2581.23728676082\t43528\n-2582.80228676082\t55720\n-2584.36728676082\t74184\n-2585.93228676082\t91992\n-2587.49728676082\t105888\n-2589.06228676082\t114512\n-2590.62628676082\t120272\n-2592.19128676082\t123640\n-2593.75628676082\t122024\n-2595.32128676082\t115504\n-2596.88628676082\t106736\n-2598.45128676082\t97864\n-2600.01628676082\t87640\n-2601.58128676082\t77312\n-2603.14628676082\t67952\n-2604.71128676082\t59464\n-2606.27628676082\t50624\n-2607.84128676082\t43672\n-2609.40628676082\t43920\n-2610.97128676082\t43880\n-2612.53628676082\t44024\n-2614.10128676082\t44192\n-2615.66628676082\t44352\n-2617.23128676082\t44048\n-2618.79628676082\t43312\n-2620.4002803902\t42128\n-2622.00450588418\t41032\n-2623.60789985113\t40696\n-2625.2124745374\t41264\n-2626.81716666296\t42000\n-2628.42193807791\t42792\n-2630.02675063237\t43880\n-2631.63156617644\t45064\n-2633.23634656023\t45872\n-2634.84105363384\t45696\n-2636.44564924738\t44992\n-2638.05009525096\t43776\n-2639.65435349467\t42608\n-2641.25838582864\t41656\n-2642.86215410296\t41328\n-2644.46562016774\t41360\n-2646.06874587309\t41520\n-2647.67149306911\t49200\n-2649.2738236059\t82296\n-2650.87569933359\t127032\n-2652.47708210226\t178368\n-2654.07793376204\t231808\n-2655.67821616301\t285120\n-2657.2778911553\t334464\n-2658.87589905919\t369856\n-2660.47424523347\t387136\n-2662.07186957376\t393344\n-2663.66930678668\t395904\n-2665.26703198027\t395456\n-2666.86491760675\t391936\n-2668.46283611837\t396608\n-2670.06065996733\t419008\n-2671.65826160588\t465280\n-2673.25551348623\t526336\n-2674.85228806062\t586624\n-2676.44845778127\t625472\n-2678.04389510041\t642304\n-2679.63847247027\t651392\n-2681.23206234307\t664256\n-2682.82633158321\t672064\n-2684.41623929172\t664448\n-2686.00135805823\t642048\n-2687.58194841108\t611776\n-2689.1582708786\t577216\n-2690.73058598911\t537408\n-2692.29815313176\t489984\n-2693.86323725773\t437248\n-2695.42509544522\t385536\n-2696.98398822256\t336256\n-2698.54017611806\t287104\n-2700.09391966008\t240512\n-2701.64547937692\t201024\n-2703.19511579694\t166656\n-2704.74308944844\t137088\n-2706.28966085977\t117720\n-2707.83509055926\t98584\n-2709.37963907523\t81576\n-2710.92356693602\t66760\n-2712.46713466996\t53440\n-2714.01060280537\t41984\n-2715.55423187058\t37808\n-2717.09813305014\t37464\n-2718.64227188502\t37832\n-2720.18669043818\t38328\n-2721.73143077261\t38720\n-2723.27653495129\t38992\n-2724.82204503719\t39120\n-2726.36701510869\t38968\n-2727.91346287142\t38728\n-2729.46044270343\t38912\n-2731.00799666769\t38984\n-2732.55616682718\t38640\n-2734.10499524488\t37584\n-2735.654523983"..b'7.39522276304\t3874\n-4228.96022276304\t3507\n-4230.52522276304\t3075\n-4232.09022276304\t2593\n-4233.65522276304\t2285\n-4235.22022276304\t2108\n-4236.78522276304\t1881\n-4238.35022276304\t1616\n-4239.91522276304\t1442\n-4241.47922276304\t1362\n-4243.04422276304\t1309\n-4244.60922276304\t1280\n-4246.17422276304\t1267\n-4247.73922276304\t1302\n-4249.30422276304\t1345\n-4250.86922276304\t1364\n-4252.43422276304\t1310\n-4253.99922276304\t1222\n-4255.56422276304\t1091\n-4257.12922276304\t896\n-4258.69422276304\t698\n-4260.25922276304\t642\n-4261.82422276304\t707\n-4263.38922276304\t711\n-4264.95422276304\t675\n-4266.51922276304\t624\n-4268.08422276304\t486\n-4269.64922276304\t406\n-4271.21422276304\t441\n-4272.77922276304\t464\n-4274.34422276304\t484\n-4275.90822276304\t531\n-4277.47322276304\t545\n-4279.03822276304\t683\n-4280.60322276304\t867\n-4282.16822276304\t954\n-4283.73322276304\t960\n-4285.29822276304\t1196\n-4286.86322276304\t1678\n-4288.42822276304\t2269\n-4289.99322276304\t2618\n-4291.55822276304\t2700\n-4293.12322276304\t2586\n-4294.68822276304\t2367\n-4296.25322276304\t2190\n-4297.81822276304\t2104\n-4299.38322276304\t1989\n-4300.94822276304\t1722\n-4302.51322276304\t1387\n-4304.07822276304\t1111\n-4305.64322276304\t977\n-4307.20822276304\t943\n-4308.77222276304\t927\n-4310.33722276304\t947\n-4311.90222276304\t910\n-4313.46722276304\t909\n-4315.03222276304\t968\n-4316.59722276304\t1005\n-4318.16222276304\t937\n-4319.72722276304\t819\n-4321.29222276304\t739\n-4322.85722276304\t736\n-4324.42222276304\t759\n-4325.98722276304\t721\n-4327.55222276304\t610\n-4329.11722276304\t439\n-4330.68222276304\t276\n-4332.24722276304\t206\n-4333.81222276304\t230\n-4335.37722276304\t309\n-4336.94222276304\t321\n-4338.50722276304\t295\n-4340.07222276304\t322\n-4341.63722276304\t430\n-4343.20122276304\t498\n-4344.76622276304\t504\n-4346.33122276304\t527\n-4347.89622276304\t631\n-4349.46122276304\t720\n-4351.02622276304\t715\n-4352.59122276304\t643\n-4354.15622276304\t654\n-4355.72122276304\t703\n-4357.28622276304\t727\n-4358.85122276304\t720\n-4360.41622276304\t654\n-4361.98122276304\t602\n-4363.54622276304\t658\n-4365.11122276304\t750\n-4366.67622276304\t781\n-4368.24122276304\t811\n-4369.80622276304\t816\n-4371.37122276304\t800\n-4372.93622276304\t770\n-4374.50122276304\t784\n-4376.06522276304\t742\n-4377.63022276304\t654\n-4379.19522276304\t632\n-4380.76022276304\t653\n-4382.32522276304\t726\n-4383.89022276304\t869\n-4385.45522276304\t937\n-4387.02022276304\t847\n-4388.58522276304\t662\n-4390.15022276304\t584\n-4391.71522276304\t671\n-4393.28022276304\t685\n-4394.84522276304\t650\n-4396.41022276304\t741\n-4397.97522276304\t797\n-4399.54022276304\t711\n-4401.10522276304\t678\n-4402.67022276304\t649\n-4404.23522276304\t683\n-4405.80022276304\t767\n-4407.36522276304\t858\n-4408.93022276304\t926\n-4410.49422276304\t1009\n-4412.05922276304\t1090\n-4413.62422276304\t1170\n-4415.18922276304\t1218\n-4416.75422276304\t1313\n-4418.31922276304\t1387\n-4419.88422276304\t1315\n-4421.44922276304\t1110\n-4423.01422276304\t984\n-4424.57922276304\t1065\n-4426.14422276304\t1127\n-4427.70922276304\t1067\n-4429.27422276304\t1116\n-4430.83922276304\t1374\n-4432.40422276304\t1494\n-4433.96922276304\t1375\n-4435.53422276304\t1176\n-4437.09922276304\t1056\n-4438.66422276304\t995\n-4440.22922276304\t973\n-4441.79422276304\t1026\n-4443.35822276304\t1065\n-4444.92322276304\t995\n-4446.48822276304\t836\n-4448.05322276304\t720\n-4449.61822276304\t716\n-4451.18322276304\t777\n-4452.74822276304\t853\n-4454.31322276304\t938\n-4455.87822276304\t1131\n-4457.44322276304\t1266\n-4459.00822276304\t1311\n-4460.57322276304\t1322\n-4462.13822276304\t1407\n-4463.70322276304\t1471\n-4465.26822276304\t1409\n-4466.83322276304\t1342\n-4468.39822276304\t1401\n-4469.96322276304\t1517\n-4471.52822276304\t1433\n-4473.09322276304\t1267\n-4474.65822276304\t1051\n-4476.22322276304\t928\n-4477.78722276304\t850\n-4479.35222276304\t821\n-4480.91722276304\t725\n-4482.48222276304\t682\n-4484.04722276304\t576\n-4485.61222276304\t583\n-4487.17722276304\t672\n-4488.74222276304\t713\n-4490.30722276304\t699\n-4491.87222276304\t667\n-4493.43722276304\t604\n-4495.00222276304\t583\n-4496.56722276304\t627\n-4498.13222276304\t693\n-4499.69722276304\t758\n-4501.26222276304\t771\n-4502.82722276304\t649\n-4504.39222276304\t565\n-4505.95722276304\t722\n' |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/cc_wt15.bpc.embedded.tab --- a/test-data/cc_wt15.bpc.embedded.tab Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,1289 +0,0 @@\n-# file_format: 'tsv'\n-# section_name: 'BPC'\n-# title: 'Base peak chromatogram'\n-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'\n-# plot_type: 'linegraph'\n-# pconfig:\n-# id: 'bpc_lineplot'\n-# title: 'Base peak chromatogram'\n-# ylab: 'Base Peak Intensity'\n-# xlab: 'Retention Time'\n-Retention Time\tBase Peak Intensity\n-2503.69308488001\t44464\n-2505.25808488001\t44632\n-2506.82308488001\t45232\n-2508.38808488001\t46200\n-2509.95308488001\t46592\n-2511.51808488001\t46376\n-2513.08308488001\t45760\n-2514.64808488001\t45632\n-2516.21308488001\t45152\n-2517.77808488001\t44280\n-2519.34308488001\t43360\n-2520.90708488001\t43768\n-2522.47208488001\t44536\n-2524.03708488001\t45072\n-2525.60208488001\t44528\n-2527.16708488001\t43632\n-2528.73208488001\t42944\n-2530.29708488001\t42520\n-2531.86208488001\t41968\n-2533.42708488001\t41312\n-2534.99208488001\t40832\n-2536.55708488001\t40624\n-2538.12208488001\t40288\n-2539.68708488001\t40144\n-2541.25208488001\t40240\n-2542.81708488001\t40488\n-2544.38208488001\t40624\n-2545.94708488001\t40688\n-2547.51208488001\t41640\n-2549.07708488001\t43840\n-2550.64208488001\t45816\n-2552.20708488001\t45248\n-2553.77208488001\t43200\n-2555.33608488001\t41936\n-2556.90108488001\t42776\n-2558.46608488001\t43472\n-2560.03108488001\t42944\n-2561.59608488001\t41400\n-2563.16108488001\t40752\n-2564.72608488001\t40560\n-2566.29108488001\t40744\n-2567.85608488001\t41488\n-2569.42108488001\t42928\n-2570.98608488001\t44352\n-2572.55108488001\t44968\n-2574.11608488001\t44832\n-2575.68108488001\t43816\n-2577.24608488001\t42704\n-2578.81108488001\t42184\n-2580.37608488001\t42864\n-2581.94108488001\t52312\n-2583.50608488001\t70008\n-2585.07108488001\t87112\n-2586.63608488001\t102376\n-2588.20008488001\t115304\n-2589.76508488001\t125384\n-2591.33008488001\t131136\n-2592.89508488001\t132096\n-2594.46008488001\t128336\n-2596.02508488001\t120840\n-2597.59008488001\t111368\n-2599.15508488001\t102296\n-2600.72008488001\t94400\n-2602.28508488001\t86608\n-2603.85008488001\t77960\n-2605.41508488001\t68544\n-2606.98008488001\t59072\n-2608.54508488001\t50408\n-2610.11008488001\t46216\n-2611.67508488001\t45656\n-2613.24008488001\t44744\n-2614.80508488001\t43880\n-2616.37008488001\t42920\n-2617.93508488001\t41824\n-2619.50008488001\t41520\n-2621.08323664293\t42464\n-2622.66535661694\t43008\n-2624.2484704446\t42256\n-2625.83156900656\t40800\n-2627.41465477536\t40128\n-2628.99773022353\t39824\n-2630.58079782361\t39656\n-2632.16386004811\t39336\n-2633.74691936957\t39456\n-2635.32997826053\t39904\n-2636.9130391935\t41000\n-2638.49610464103\t41752\n-2640.07917707564\t41784\n-2641.66225896986\t41568\n-2643.24535279622\t41952\n-2644.82846102725\t42552\n-2646.41158613548\t43008\n-2647.99473059345\t67248\n-2649.57789687368\t104320\n-2651.1610874487\t148800\n-2652.74430479104\t199872\n-2654.32755137323\t257088\n-2655.90981797773\t312128\n-2657.49313043459\t356928\n-2659.07647954731\t388992\n-2660.65986778842\t406848\n-2662.24329763045\t407360\n-2663.82662043703\t397824\n-2665.40972747004\t395968\n-2666.99268104941\t409600\n-2668.5755434951\t437056\n-2670.15837712702\t475008\n-2671.74124426513\t522112\n-2673.32420722935\t568256\n-2674.90732833963\t610304\n-2676.4906699159\t647616\n-2678.07429427809\t682816\n-2679.65826374615\t705920\n-2681.24264064001\t709568\n-2682.82780937765\t697408\n-2684.41329800875\t682688\n-2685.99992572252\t668928\n-2687.58718990559\t646464\n-2689.17458794457\t615360\n-2690.76060337453\t579584\n-2692.34676200243\t538560\n-2693.9314023906\t485696\n-2695.51423451065\t428096\n-2697.09529149161\t375808\n-2698.67460646253\t329920\n-2700.25221255246\t285888\n-2701.82814289044\t241664\n-2703.4024306055\t199296\n-2704.9751088267\t161472\n-2706.54621068307\t129928\n-2708.11576930366\t107776\n-2709.68381781752\t90320\n-2711.25038935368\t75720\n-2712.81551704119\t62600\n-2714.37923400909\t51632\n-2715.94157338643\t42784\n-2717.50256830224\t43368\n-2719.06225188558\t43000\n-2720.62065726547\t41624\n-2722.17781757098\t39880\n-2723.73277209484\t38296\n-2725.28754238135\t37568\n-2726.84116695942\t37856\n-2728.39367895811\t38736\n-2729.94511150645\t39696\n-2731.49549773349\t40576\n-2733.04487076827\t41336\n-2734.59326373983\t42240\n-2736.14070977"..b'73915089905\t4742\n-4231.30415089905\t3929\n-4232.86915089905\t3246\n-4234.43415089905\t2973\n-4235.99915089905\t2620\n-4237.56415089905\t2296\n-4239.12915089905\t2214\n-4240.69415089905\t2221\n-4242.25815089905\t2112\n-4243.82315089905\t1787\n-4245.38815089905\t1594\n-4246.95315089905\t1593\n-4248.51815089905\t1604\n-4250.08315089905\t1417\n-4251.64815089905\t1264\n-4253.21315089905\t1229\n-4254.77815089905\t1307\n-4256.34315089905\t1303\n-4257.90815089905\t1247\n-4259.47315089905\t1232\n-4261.03815089905\t1225\n-4262.60315089905\t1173\n-4264.16815089905\t1066\n-4265.73315089905\t989\n-4267.29815089905\t884\n-4268.86315089905\t826\n-4270.42815089905\t765\n-4271.99315089905\t819\n-4273.55815089905\t908\n-4275.12215089905\t959\n-4276.68715089905\t933\n-4278.25215089905\t903\n-4279.81715089905\t862\n-4281.38215089905\t785\n-4282.94715089905\t692\n-4284.51215089905\t567\n-4286.07715089905\t405\n-4287.64215089905\t300\n-4289.20715089905\t293\n-4290.77215089905\t344\n-4292.33715089905\t323\n-4293.90215089905\t334\n-4295.46715089905\t343\n-4297.03215089905\t295\n-4298.59715089905\t264\n-4300.16215089905\t251\n-4301.72715089905\t230\n-4303.29215089905\t216\n-4304.85715089905\t170\n-4306.42215089905\t145\n-4307.98715089905\t145\n-4309.55115089905\t145\n-4311.11615089905\t162\n-4312.68115089905\t190\n-4314.24615089905\t173\n-4315.81115089905\t159\n-4317.37615089905\t156\n-4318.94115089905\t160\n-4320.50615089905\t166\n-4322.07115089905\t190\n-4323.63615089905\t216\n-4325.20115089905\t268\n-4326.76615089905\t298\n-4328.33115089905\t366\n-4329.89615089905\t442\n-4331.46115089905\t440\n-4333.02615089905\t310\n-4334.59115089905\t284\n-4336.15615089905\t260\n-4337.72115089905\t280\n-4339.28615089905\t295\n-4340.85115089905\t230\n-4342.41515089905\t230\n-4343.98015089905\t205\n-4345.54515089905\t203\n-4347.11015089905\t229\n-4348.67515089905\t224\n-4350.24015089905\t213\n-4351.80515089905\t242\n-4353.37015089905\t243\n-4354.93515089905\t230\n-4356.50015089905\t205\n-4358.06515089905\t188\n-4359.63015089905\t150\n-4361.19515089905\t180\n-4362.76015089905\t209\n-4364.32515089905\t218\n-4365.89015089905\t228\n-4367.45515089905\t275\n-4369.02015089905\t326\n-4370.58515089905\t336\n-4372.15015089905\t327\n-4373.71515089905\t270\n-4375.28015089905\t237\n-4376.84415089905\t317\n-4378.40915089905\t297\n-4379.97415089905\t292\n-4381.53915089905\t282\n-4383.10415089905\t265\n-4384.66915089905\t244\n-4386.23415089905\t254\n-4387.79915089905\t242\n-4389.36415089905\t245\n-4390.92915089905\t282\n-4392.49415089905\t272\n-4394.05915089905\t261\n-4395.62415089905\t267\n-4397.18915089905\t296\n-4398.75415089905\t311\n-4400.31915089905\t359\n-4401.88415089905\t497\n-4403.44915089905\t574\n-4405.01415089905\t551\n-4406.57915089905\t473\n-4408.14415089905\t405\n-4409.70815089905\t419\n-4411.27315089905\t388\n-4412.83815089905\t383\n-4414.40315089905\t394\n-4415.96815089905\t438\n-4417.53315089905\t583\n-4419.09815089905\t705\n-4420.66315089905\t736\n-4422.22815089905\t736\n-4423.79315089905\t799\n-4425.35815089905\t882\n-4426.92315089905\t865\n-4428.48815089905\t820\n-4430.05315089905\t815\n-4431.61815089905\t910\n-4433.18315089905\t959\n-4434.74815089905\t946\n-4436.31315089905\t955\n-4437.87815089905\t950\n-4439.44315089905\t982\n-4441.00815089905\t1030\n-4442.57315089905\t1127\n-4444.13715089905\t1218\n-4445.70215089905\t1305\n-4447.26715089905\t1363\n-4448.83215089905\t1532\n-4450.39715089905\t1694\n-4451.96215089905\t1884\n-4453.52715089905\t2156\n-4455.09215089905\t2656\n-4456.65715089905\t3328\n-4458.22215089905\t3827\n-4459.78715089905\t3969\n-4461.35215089905\t4055\n-4462.91715089905\t4262\n-4464.48215089905\t4494\n-4466.04715089905\t4501\n-4467.61215089905\t4404\n-4469.17715089905\t4316\n-4470.74215089905\t4290\n-4472.30715089905\t4232\n-4473.87215089905\t4215\n-4475.43715089905\t4443\n-4477.00115089905\t4838\n-4478.56615089905\t4920\n-4480.13115089905\t4294\n-4481.69615089905\t3437\n-4483.26115089905\t3096\n-4484.82615089905\t3312\n-4486.39115089905\t3426\n-4487.95615089905\t3085\n-4489.52115089905\t2750\n-4491.08615089905\t2696\n-4492.65115089905\t2920\n-4494.21615089905\t3119\n-4495.78115089905\t3322\n-4497.34615089905\t3463\n-4498.91115089905\t3313\n-4500.47615089905\t3184\n-4502.04115089905\t3217\n-4503.60615089905\t3240\n-4505.17115089905\t3288\n-4506.73615089905\t3582\n-4508.30115089905\t3963\n' |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/cutadapt_stats.tabular --- a/test-data/cutadapt_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/fastp_stats.tabular --- a/test-data/fastp_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/fastqc_stats.tabular --- a/test-data/fastqc_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/featureCounts_stats.tabular --- a/test-data/featureCounts_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/flexbar_stats.tabular --- a/test-data/flexbar_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/gatk_varianteval_stats.tabular --- a/test-data/gatk_varianteval_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +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 f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_deduplicator.txt --- a/test-data/hicup_deduplicator.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques -Sample-1.A007.C8DRAANXX.s_2.r_1_2.filt.bam 7029431 6978457 876396 4591811 1510250 -Sample-1.A002.C8DRAANXX.s_2.r_1_2.filt.bam 8935388 8864466 1159324 5742469 1962673 -Sample-1.A005.C8DRAANXX.s_2.r_1_2.filt.bam 11314841 11219537 1495237 7243835 2480465 -Sample-1.A019.C8DRAANXX.s_2.r_1_2.filt.bam 11766363 11658185 1811982 7779338 2066865 -Sample-1.A012.C8DRAANXX.s_2.r_1_2.filt.bam 11705308 11609411 1261011 7003201 3345199 -Sample-1.A006.C8DRAANXX.s_2.r_1_2.filt.bam 13106391 12998003 2043926 8107586 2846491 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_filter.txt --- a/test-data/hicup_filter.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size -Sample-1.A002.C8DRAANXX.s_2.r_1_2.pair.bam 14383198 8935388 1169666 5787588 1978134 5447810 136087 530246 2442480 834795 48328 1455874 -Sample-1.A007.C8DRAANXX.s_2.r_1_2.pair.bam 14621513 7029431 882929 4625450 1521052 7592082 157241 452563 4031859 771757 37367 2141295 -Sample-1.A005.C8DRAANXX.s_2.r_1_2.pair.bam 15245021 11314841 1509270 7304795 2500776 3930180 187236 298334 1580105 924315 59919 880271 -Sample-1.A019.C8DRAANXX.s_2.r_1_2.pair.bam 16053923 11766363 1830414 7850293 2085656 4287560 223187 305385 1541376 1070842 72067 1074703 -Sample-1.A006.C8DRAANXX.s_2.r_1_2.pair.bam 18473566 13106391 2063334 8173491 2869566 5367175 220527 408217 2075370 961388 65086 1636587 -Sample-1.A012.C8DRAANXX.s_2.r_1_2.pair.bam 19070455 11705308 1272882 7060212 3372214 7365147 163868 663463 3810160 976378 55368 1695910 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_mapper.txt --- a/test-data/hicup_mapper.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired -Sample-1.A006.C8DRAANXX.s_2.r_1.trunc.fastq.gz 34760244 579570 1.7 25926210 74.6 5230796 15.0 3023668 8.7 18473566 53.1 -Sample-1.A006.C8DRAANXX.s_2.r_2.trunc.fastq.gz 34760244 539500 1.6 25637256 73.8 5121683 14.7 3461805 10.0 18473566 53.1 -Sample-1.A005.C8DRAANXX.s_2.r_1.trunc.fastq.gz 26780491 431302 1.6 20379141 76.1 4263954 15.9 1706094 6.4 15245021 56.9 -Sample-1.A005.C8DRAANXX.s_2.r_2.trunc.fastq.gz 26780491 407260 1.5 20071745 74.9 4167422 15.6 2134064 8.0 15245021 56.9 -Sample-1.A012.C8DRAANXX.s_2.r_1.trunc.fastq.gz 35472550 526747 1.5 26504291 74.7 5362349 15.1 3079163 8.7 19070455 53.8 -Sample-1.A012.C8DRAANXX.s_2.r_2.trunc.fastq.gz 35472550 494718 1.4 26142222 73.7 5264577 14.8 3571033 10.1 19070455 53.8 -Sample-1.A002.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28754600 751623 2.6 21072845 73.3 4475271 15.6 2454861 8.5 14383198 50.0 -Sample-1.A002.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28754600 698375 2.4 20505141 71.3 4336149 15.1 3214935 11.2 14383198 50.0 -Sample-1.A007.C8DRAANXX.s_2.r_1.trunc.fastq.gz 31000250 368533 1.2 22327487 72.0 4263821 13.8 4040409 13.0 14621513 47.2 -Sample-1.A007.C8DRAANXX.s_2.r_2.trunc.fastq.gz 31000250 338254 1.1 21828226 70.4 4140992 13.4 4692778 15.1 14621513 47.2 -Sample-1.A019.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28583413 519100 1.8 21667602 75.8 4404215 15.4 1992496 7.0 16053923 56.2 -Sample-1.A019.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28583413 488517 1.7 21491634 75.2 4342639 15.2 2260623 7.9 16053923 56.2 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_truncater.txt --- a/test-data/hicup_truncater.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence -Sample-1.A002.C8DRAANXX.s_2.r_1.fq 28754600 7548969 26.25 21205631 73.75 58.69 -Sample-1.A002.C8DRAANXX.s_2.r_2.fq 28754600 7446167 25.90 21308433 74.10 59.65 -Sample-1.A006.C8DRAANXX.s_2.r_2.fq 34760244 10523907 30.28 24236337 69.72 66.68 -Sample-1.A012.C8DRAANXX.s_2.r_2.fq 35472550 9050477 25.51 26422073 74.49 66.30 -Sample-1.A006.C8DRAANXX.s_2.r_1.fq 34760244 10420308 29.98 24339936 70.02 65.67 -Sample-1.A012.C8DRAANXX.s_2.r_1.fq 35472550 8999621 25.37 26472929 74.63 65.39 -Sample-1.A005.C8DRAANXX.s_2.r_2.fq 26780491 8436781 31.50 18343710 68.50 67.02 -Sample-1.A005.C8DRAANXX.s_2.r_1.fq 26780491 8361813 31.22 18418678 68.78 66.22 -Sample-1.A019.C8DRAANXX.s_2.r_2.fq 28583413 9321837 32.61 19261576 67.39 66.38 -Sample-1.A019.C8DRAANXX.s_2.r_1.fq 28583413 9151107 32.02 19432306 67.98 65.11 -Sample-1.A007.C8DRAANXX.s_2.r_1.fq 31000250 6212988 20.04 24787262 79.96 65.01 -Sample-1.A007.C8DRAANXX.s_2.r_2.fq 31000250 6187239 19.96 24813011 80.04 65.94 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Sample unpaired_total overall_alignment_rate unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi -hisat2_1 99978 96.15 86176 3849 9953 -hisat2_2 99978 96.15 86176 3849 9953 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/htseq_stats.tabular --- a/test-data/htseq_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +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 f7985e0479b9 -r c1a4b5f3b432 test-data/kallisto_stats.tabular --- a/test-data/kallisto_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Sample percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads fragment_length -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 58016047.0 9484959.0 48531088.0 167.866 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 70152623.0 10871703.0 59280920.0 169.418 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/macs_stats.tabular --- a/test-data/macs_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Sample fragment_size treatment_fragments_total treatment_fragments_after_filtering treatment_max_duplicates treatment_redundant_rate control_fragments_total control_fragments_after_filtering control_max_duplicates control_redundant_rate d -treat1 100.0 199977.0 199583.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 -treat2 100.0 100000.0 99795.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_AlignmentSummaryMetrics_stats.tabular --- a/test-data/picard_AlignmentSummaryMetrics_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/picard_RnaSeqMetrics_stats.tabular --- a/test-data/picard_RnaSeqMetrics_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/picard_baseContent_stats.tabular --- a/test-data/picard_baseContent_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/picard_dups_stats.tabular --- a/test-data/picard_dups_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/picard_insertSize_stats.tabular --- a/test-data/picard_insertSize_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample SAMPLE_NAME MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP -dataset_197_FR dataset_197 194.0 63.0 100.0 5331452.0 271.809759 196.076488 311788.0 FR 25.0 47.0 69.0 91.0 127.0 343.0 941.0 1515.0 2585.0 16663.0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/post_aligner_soft_report.html --- a/test-data/post_aligner_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,7363 +0,0 @@\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 f7985e0479b9 -r c1a4b5f3b432 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/pre_alignment_soft_report.html --- a/test-data/pre_alignment_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,5990 +0,0 @@\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 f7985e0479b9 -r c1a4b5f3b432 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -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 Slamdunk_mqc-generalstats-slamdunk-counted Slamdunk_mqc-generalstats-slamdunk-retained Slamdunk_mqc-generalstats-slamdunk-mapped Slamdunk_mqc-generalstats-slamdunk-sequenced 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 -reads1 16 12 12 12 -reads2 12 6 6 6 -result_right 45.26066350710901 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/prokka_stats.tabular --- a/test-data/prokka_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -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 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/qualimap_bamqc_genome_results.tabular --- a/test-data/qualimap_bamqc_genome_results.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample bam_file total_reads mapped_reads mapped_bases sequenced_bases mean_insert_size median_insert_size mean_mapping_quality general_error_rate percentage_aligned -x_bam x_bam 1248774.0 1242183.0 366875582.0 366823893.0 1097.678 524.0 58.4552 0.0098 99.4722023360512 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/quast_stats.tabular --- a/test-data/quast_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/rsem.txt --- a/test-data/rsem.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,57 +0,0 @@ -2302013 30752387 0 33054400 -30113921 638466 13832652 -65457099 3 -0 2302013 -1 16919735 -2 6224666 -3 3186612 -4 1664884 -5 1091224 -6 555346 -7 358669 -8 245597 -9 98797 -10 65875 -11 83793 -12 46956 -13 26998 -14 45559 -15 33388 -16 11464 -17 7678 -18 12949 -19 22852 -20 16386 -21 6725 -22 16252 -23 3943 -24 3304 -25 18 -26 1 -27 11 -28 27 -29 37 -30 56 -31 115 -32 146 -33 210 -34 18 -35 128 -36 5 -37 47 -38 129 -39 81 -40 1231 -41 284 -42 27 -43 112 -44 6 -45 4 -46 1 -47 1 -48 7 -53 2 -71 24 -73 1 -77 6 -Inf 0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/salmon_flenDist.txt --- a/test-data/salmon_flenDist.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2 +0,0 @@\n-8.54794e-14\t8.88776e-14\t9.23963e-14\t9.60394e-14\t9.98106e-14\t1.03714e-13\t1.07752e-13\t1.11931e-13\t1.16253e-13\t1.20724e-13\t1.25347e-13\t1.30126e-13\t1.35067e-13\t1.40173e-13\t1.4545e-13\t1.50902e-13\t1.56533e-13\t1.6235e-13\t1.68356e-13\t1.74557e-13\t1.80958e-13\t1.87565e-13\t1.94382e-13\t2.01416e-13\t2.08672e-13\t2.16156e-13\t2.23872e-13\t2.31828e-13\t2.4003e-13\t2.48482e-13\t2.57192e-13\t2.66166e-13\t2.7541e-13\t2.8493e-13\t2.94734e-13\t3.04827e-13\t3.15216e-13\t3.25909e-13\t3.36912e-13\t3.48231e-13\t3.59875e-13\t3.7185e-13\t3.84164e-13\t3.96823e-13\t4.09835e-13\t4.23208e-13\t4.36949e-13\t4.51066e-13\t4.65566e-13\t4.80457e-13\t4.95747e-13\t5.11443e-13\t5.27555e-13\t5.44088e-13\t5.61052e-13\t5.78455e-13\t5.96304e-13\t6.14608e-13\t6.33375e-13\t6.52613e-13\t6.7233e-13\t6.92535e-13\t7.13235e-13\t7.34439e-13\t7.56156e-13\t7.78393e-13\t8.01159e-13\t8.24462e-13\t8.4831e-13\t8.72712e-13\t8.97675e-13\t9.23208e-13\t9.49319e-13\t9.76016e-13\t1.00331e-12\t1.0312e-12\t1.0597e-12\t1.08882e-12\t1.11857e-12\t1.14895e-12\t1.17997e-12\t1.21163e-12\t1.24396e-12\t1.27694e-12\t1.3106e-12\t1.34493e-12\t1.37995e-12\t1.41566e-12\t1.45206e-12\t1.48917e-12\t1.52699e-12\t1.56552e-12\t1.60477e-12\t1.64476e-12\t1.68547e-12\t1.72692e-12\t1.76912e-12\t1.81206e-12\t3.29651e-05\t0.00018966\t0.000505733\t0.000852837\t0.00107903\t0.00117955\t0.0012102\t0.00118557\t0.00113454\t0.00110862\t0.00112071\t0.001135\t0.00112018\t0.00109392\t0.00110592\t0.00116328\t0.00120188\t0.00119639\t0.00120395\t0.00123364\t0.00121303\t0.00113283\t0.00106575\t0.0010294\t0.00101907\t0.00107787\t0.00117117\t0.00122155\t0.00126292\t0.001322\t0.00132568\t0.00125944\t0.0012187\t0.00122729\t0.00122764\t0.00125145\t0.00130243\t0.00129889\t0.00129122\t0.00136001\t0.00143294\t0.00144178\t0.00141998\t0.00139328\t0.00136291\t0.00137291\t0.00143527\t0.00148261\t0.00148996\t0.0014951\t0.00152389\t0.00155437\t0.00155677\t0.00157319\t0.00161304\t0.00161234\t0.00155184\t0.00146051\t0.00140614\t0.00145661\t0.00161047\t0.00177332\t0.00183641\t0.00180834\t0.00175883\t0.00171746\t0.00167723\t0.00163458\t0.00160951\t0.00161254\t0.00166641\t0.00181422\t0.00201421\t0.00213023\t0.00209065\t0.00197041\t0.00188134\t0.00184267\t0.00181737\t0.00181102\t0.00185763\t0.00195455\t0.00203258\t0.00205324\t0.00208063\t0.00211824\t0.00209545\t0.00206314\t0.00209033\t0.00209553\t0.00204238\t0.00203362\t0.00209684\t0.00217598\t0.00227147\t0.00238701\t0.00243673\t0.00232052\t0.00213204\t0.00209969\t0.00224284\t0.00240577\t0.00252668\t0.0025933\t0.002587\t0.00256927\t0.00259717\t0.00263285\t0.00263222\t0.00258247\t0.00252205\t0.00252088\t0.00256024\t0.00259275\t0.0026236\t0.00266515\t0.00270772\t0.0027058\t0.00268944\t0.0027414\t0.00278318\t0.00271033\t0.00262591\t0.0026647\t0.00279403\t0.00290929\t0.00296039\t0.00295669\t0.00293271\t0.0028987\t0.0028311\t0.00277538\t0.00282072\t0.00293968\t0.00304533\t0.00310031\t0.00310671\t0.00309913\t0.00308228\t0.00302181\t0.00292959\t0.00285281\t0.00281429\t0.00282158\t0.00288\t0.00296587\t0.00307507\t0.00321613\t0.00327918\t0.00318075\t0.00306869\t0.00304228\t0.00299811\t0.00295958\t0.0030338\t0.00314258\t0.0032122\t0.00330145\t0.00337388\t0.00331331\t0.00319232\t0.00317648\t0.00324005\t0.00325072\t0.0032239\t0.0032372\t0.00321137\t0.00309323\t0.00303576\t0.00311229\t0.00316625\t0.00309878\t0.00297703\t0.00288252\t0.00287056\t0.00294284\t0.00301172\t0.00296646\t0.00283922\t0.00281166\t0.00291487\t0.00303261\t0.00313036\t0.00314853\t0.00305521\t0.00298739\t0.00299062\t0.00297359\t0.00291442\t0.00284123\t0.00280557\t0.00284507\t0.00290229\t0.00289053\t0.00282273\t0.00278903\t0.00281558\t0.00287164\t0.00292608\t0.0029143\t0.00284278\t0.00282664\t0.00288701\t0.00295603\t0.00298966\t0.00294605\t0.00285187\t0.00278262\t0.00273969\t0.00271188\t0.00271717\t0.00273696\t0.00275274\t0.00275838\t0.00274122\t0.00271621\t0.00268619\t0.00263703\t0.00257204\t0.0025213\t0.00253616\t0.00260787\t0.0026735\t0.00271237\t0.00275647\t0.00279131\t0.00271385\t0.00253059\t0.00241637\t0.00242943\t0.00249082\t0.00257038\t0.00263479\t0.00266551\t0.00267075\t0.00263741\t0.002596\t0.00253267\t0.00242838\t0.00239026\t0.00244334\t0.00245337\t0.00238774\t0.00235235\t0.00236255\t0.00235744\t0.0023223\t0.00229\t0.00232159\t0.00236911\t0.00234045\t0.00229188\t0.00228046\t0.00228006\t0.00230137\t0.00234177\t0.00233269\t0.00226339\t0.0021914'..b'\t3.48633e-06\t6.56158e-06\t6.56591e-06\t3.83529e-06\t1.87558e-06\t2.86313e-06\t5.46522e-06\t6.77583e-06\t6.76114e-06\t5.96453e-06\t3.46521e-06\t8.60546e-07\t8.57557e-07\t3.41456e-06\t5.12027e-06\t3.97947e-06\t3.37465e-06\t5.5051e-06\t8.12692e-06\t8.17751e-06\t4.99229e-06\t1.70417e-06\t4.16364e-07\t1.04091e-07\t8.48451e-20\t8.48451e-20\t1.03855e-06\t4.17877e-06\t7.31893e-06\t8.25894e-06\t7.07274e-06\t3.98182e-06\t1.10885e-06\t4.78174e-07\t7.17261e-07\t4.78174e-07\t1.06162e-06\t3.76832e-06\t5.65248e-06\t3.76832e-06\t1.00433e-06\t9.46158e-07\t3.69878e-06\t6.57856e-06\t6.0715e-06\t2.84656e-06\t5.40835e-07\t6.62769e-07\t2.64063e-06\t3.95989e-06\t2.63993e-06\t6.65929e-07\t2.3786e-08\t3.5679e-08\t2.3786e-08\t5.9465e-09\t8.48451e-20\t8.48451e-20\t1.05325e-06\t4.213e-06\t6.31951e-06\t4.213e-06\t1.74237e-06\t2.75646e-06\t4.14557e-06\t2.79999e-06\t7.54417e-07\t4.35348e-08\t1.08837e-08\t1.62467e-06\t6.4987e-06\t9.74804e-06\t6.4987e-06\t1.62467e-06\t2.42376e-07\t9.69503e-07\t1.45515e-06\t9.73101e-07\t2.47772e-07\t3.59728e-09\t2.08228e-06\t8.32552e-06\t1.25152e-05\t8.43337e-06\t2.53305e-06\t1.26743e-06\t1.76634e-06\t1.16823e-06\t9.73446e-07\t2.64779e-06\t3.92848e-06\t2.60459e-06\t6.81238e-07\t1.34953e-07\t2.17296e-07\t1.64686e-07\t5.60377e-08\t2.95843e-07\t1.15959e-06\t1.82339e-06\t2.39241e-06\t4.38112e-06\t6.7061e-06\t7.6585e-06\t6.95299e-06\t4.13776e-06\t1.10966e-06\t5.44951e-07\t2.05945e-06\t3.08987e-06\t2.06224e-06\t5.19564e-07\t4.87571e-09\t1.20166e-07\t4.67429e-07\t7.15222e-07\t5.67288e-07\t3.57226e-07\t7.34211e-07\t1.98274e-06\t2.77314e-06\t1.8253e-06\t5.34391e-07\t3.12261e-07\t4.68391e-07\t3.12261e-07\t7.80652e-08\t4.91325e-08\t1.9653e-07\t2.94795e-07\t1.96778e-07\t5.01263e-08\t1.49069e-09\t9.9379e-10\t2.48448e-10\t8.48451e-20\t8.48451e-20\t1.28319e-06\t5.13871e-06\t7.72294e-06\t5.16845e-06\t1.30698e-06\t5.9465e-09\t6.45033e-08\t4.1415e-07\t1.01157e-06\t1.21721e-06\t7.78569e-07\t2.90415e-07\t8.9519e-08\t1.62661e-06\t7.55928e-06\t1.41948e-05\t1.33201e-05\t6.37014e-06\t1.43714e-06\t1.9653e-07\t4.91325e-08\t8.48451e-20\t1.40225e-09\t3.01961e-08\t1.06762e-07\t1.53132e-07\t1.48883e-07\t2.21117e-07\t2.94795e-07\t1.9653e-07\t1.52023e-07\t1.4224e-06\t4.66068e-06\t6.47657e-06\t4.14623e-06\t1.2079e-06\t7.88265e-07\t1.1824e-06\t7.88265e-07\t1.97066e-07\t1.13356e-09\t4.53426e-09\t7.40038e-08\t8.39303e-07\t2.66819e-06\t3.66457e-06\t2.33104e-06\t5.65959e-07\t8.48451e-20\t5.75979e-08\t2.30392e-07\t3.45587e-07\t2.32447e-07\t6.58203e-08\t1.23336e-08\t1.27549e-08\t2.01854e-08\t2.71947e-08\t1.81298e-08\t4.53244e-09\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t1.56137e-07\t6.82145e-07\t1.16721e-06\t9.70134e-07\t3.86528e-07\t5.75979e-08\t9.89308e-07\t3.95723e-06\t5.95252e-06\t4.56652e-06\t3.25974e-06\t3.32229e-06\t2.6434e-06\t2.3679e-06\t2.73795e-06\t1.8253e-06\t4.56325e-07\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t4.52923e-08\t1.81169e-07\t2.71754e-07\t1.81169e-07\t4.52923e-08\t8.48451e-20\t2.42376e-07\t9.69503e-07\t1.45426e-06\t9.69503e-07\t2.42376e-07\t8.48451e-20\t1.27948e-07\t5.11793e-07\t7.72222e-07\t5.29923e-07\t3.56237e-07\t8.22506e-07\t1.2111e-06\t8.04377e-07\t2.01094e-07\t1.19543e-07\t4.85833e-07\t7.47897e-07\t5.59316e-07\t2.9093e-07\t2.18785e-07\t1.4075e-07\t3.51876e-08\t8.48451e-20\t1.7085e-09\t6.83399e-09\t1.0251e-08\t4.48392e-07\t1.76794e-06\t2.64935e-06\t1.76623e-06\t4.41558e-07\t2.28063e-07\t9.20891e-07\t1.40294e-06\t9.70858e-07\t3.1919e-07\t1.67271e-07\t2.04131e-07\t9.36586e-07\t3.27659e-06\t4.87062e-06\t3.25897e-06\t8.59342e-07\t7.1358e-08\t4.7572e-08\t1.1893e-08\t8.48451e-20\t1.19543e-07\t4.78174e-07\t7.17261e-07\t4.78174e-07\t1.19543e-07\t8.48451e-20\t8.48451e-20\t8.48451e-20\t3.652e-07\t1.4608e-06\t2.1912e-06\t1.4608e-06\t3.652e-07\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t2.88646e-09\t1.31089e-07\t4.95492e-07\t7.28806e-07\t4.8106e-07\t1.19543e-07\t8.48451e-20\t2.11966e-06\t8.47864e-06\t1.2718e-05\t8.49079e-06\t2.16829e-06\t3.62843e-07\t1.88217e-06\t4.44733e-06\t5.20328e-06\t2.98569e-06\t6.76004e-07\t8.22241e-09\t1.23336e-08\t8.22241e-09\t4.1112e-09\t8.22241e-09\t1.23336e-08\t8.22241e-09\t2.0556e-09\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t8.48451e-20\t5.08647e-07\t2.89843e-06\t6.66338e-06\t7.84217e-06\t4.90082e-06\t2.61356e-05\t9.87451e-05\t0.000147884\n-\n' |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/salmon_meta_info.json --- a/test-data/salmon_meta_info.json Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -{ - "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 f7985e0479b9 -r c1a4b5f3b432 test-data/samblaster_stats.tabular --- a/test-data/samblaster_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample n_nondups n_tot n_dups pct_dups -virtual-normal 77 78 1 1.28 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/samtools_flagstat_stats.tabular --- a/test-data/samtools_flagstat_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/samtools_stats_stats.tabular --- a/test-data/samtools_stats_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/slamdunk_readrates_plus.tabular --- a/test-data/slamdunk_readrates_plus.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Sample A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G -slamdunk_reads1_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.7735849056603774 0.0 -slamdunk_reads2_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.260869565217391 0.0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/snpeff_stats.tabular --- a/test-data/snpeff_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2 +0,0 @@\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 f7985e0479b9 -r c1a4b5f3b432 test-data/sortmerna_stats.tabular --- a/test-data/sortmerna_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -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 f7985e0479b9 -r c1a4b5f3b432 test-data/star_stats.tabular --- a/test-data/star_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample mismatch_rate avg_input_read_length num_annotated_splices multimapped_toomany_percent num_splices uniquely_mapped uniquely_mapped_percent multimapped multimapped_toomany unmapped_tooshort multimapped_percent num_ATAC_splices unmapped_tooshort_percent total_reads unmapped_mismatches num_noncanonical_splices insertion_rate unmapped_other_percent num_GTAG_splices insertion_length deletion_length deletion_rate unmapped_other unmapped_mismatches_percent num_GCAG_splices avg_mapped_read_length -star_log 1.73 75.0 0.0 0.0 47.0 89.0 89.0 1.0 0.0 10 1.0 0.0 10.0 100.0 0 0.0 0.0 0.0 47.0 0.0 0.0 0.0 0 0.0 0.0 74.8 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/tophat_stats.tabular --- a/test-data/tophat_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample total_reads concordant_aligned_percent unaligned_total aligned_total aligned_multimap aligned_discordant overall_aligned_percent aligned_not_multimapped_discordant -tophat_align 316390.0 99.0 2985.0 313405.0 5638.0 34.0 99.5 307733.0 |
| b |
| diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/trimmomatic_stats.tabular --- a/test-data/trimmomatic_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Sample input_reads surviving dropped surviving_pct dropped_pct -C2 39733090.0 32590558.0 7142532.0 82.02 17.98 |