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Remove the extra data files

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This commit is contained in:
Abhinav Sharma 2020-12-04 20:15:48 +05:30
parent 3da7aec183
commit 27b4b29976
8 changed files with 3 additions and 10146 deletions
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1
.github/workflows/multiqc.yml vendored
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# Test the module
- run: pytest --tag multiqc --symlink --wt 2

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tests/data/multiqc/multiqc_data/multiqc.log
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[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: /usr/local/lib/python3.8/site-packages/multiqc_config.yaml
[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: /.multiqc_config.yaml
[2020-11-28 16:22:29,678] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2020-11-28 16:22:29,678] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc .
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Latest MultiQC version is v1.9
[2020-11-28 16:22:30,040] multiqc [INFO ] This is MultiQC v1.9
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Command : /usr/local/bin/multiqc .
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Working dir : /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52
[2020-11-28 16:22:30,040] multiqc [INFO ] Template : default
[2020-11-28 16:22:30,040] multiqc [DEBUG ] Running Python 3.8.5 | packaged by conda-forge | (default, Jul 24 2020, 01:25:15) [GCC 7.5.0]
[2020-11-28 16:22:30,041] multiqc [INFO ] Searching : /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52
[2020-11-28 16:22:30,041] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean
[2020-11-28 16:22:30,041] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp2h0fqr8s
[2020-11-28 16:22:30,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,126] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: test_2_fastqc.html
[2020-11-28 16:22:30,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: .command.run
[2020-11-28 16:22:30,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,185] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: test_1_fastqc.html
[2020-11-28 16:22:30,607] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.0
[2020-11-28 16:22:30,607] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.0
[2020-11-28 16:22:30,608] multiqc [DEBUG ] No samples found: custom_content
[2020-11-28 16:22:30,611] multiqc [DEBUG ] No samples found: conpair
[2020-11-28 16:22:30,613] multiqc [DEBUG ] No samples found: peddy
[2020-11-28 16:22:30,616] multiqc [DEBUG ] No samples found: somalier
[2020-11-28 16:22:30,618] multiqc [DEBUG ] No samples found: methylQA
[2020-11-28 16:22:30,621] multiqc [DEBUG ] No samples found: mosdepth
[2020-11-28 16:22:30,624] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2020-11-28 16:22:30,626] multiqc [DEBUG ] No samples found: qualimap
[2020-11-28 16:22:30,629] multiqc [DEBUG ] No samples found: preseq
[2020-11-28 16:22:30,631] multiqc [DEBUG ] No samples found: quast
[2020-11-28 16:22:30,633] multiqc [DEBUG ] No samples found: qorts
[2020-11-28 16:22:30,636] multiqc [DEBUG ] No samples found: rna_seqc
[2020-11-28 16:22:30,638] multiqc [DEBUG ] No samples found: rockhopper
[2020-11-28 16:22:30,640] multiqc [DEBUG ] No samples found: rsem
[2020-11-28 16:22:30,644] multiqc [DEBUG ] No samples found: rseqc
[2020-11-28 16:22:30,647] multiqc [DEBUG ] No samples found: busco
[2020-11-28 16:22:30,649] multiqc [DEBUG ] No samples found: goleft_indexcov
[2020-11-28 16:22:30,651] multiqc [DEBUG ] No samples found: disambiguate
[2020-11-28 16:22:30,654] multiqc [DEBUG ] No samples found: supernova
[2020-11-28 16:22:30,658] multiqc [DEBUG ] No samples found: deeptools
[2020-11-28 16:22:30,660] multiqc [DEBUG ] No samples found: sargasso
[2020-11-28 16:22:30,663] multiqc [DEBUG ] No samples found: verifybamid
[2020-11-28 16:22:30,665] multiqc [DEBUG ] No samples found: mirtrace
[2020-11-28 16:22:30,667] multiqc [DEBUG ] No samples found: happy
[2020-11-28 16:22:30,670] multiqc [DEBUG ] No samples found: mirtop
[2020-11-28 16:22:30,673] multiqc [DEBUG ] No samples found: homer
[2020-11-28 16:22:30,675] multiqc [DEBUG ] No samples found: macs2
[2020-11-28 16:22:30,677] multiqc [DEBUG ] No samples found: theta2
[2020-11-28 16:22:30,680] multiqc [DEBUG ] No samples found: snpeff
[2020-11-28 16:22:30,683] multiqc [DEBUG ] No samples found: gatk
[2020-11-28 16:22:30,685] multiqc [DEBUG ] No samples found: htseq
[2020-11-28 16:22:30,687] multiqc [DEBUG ] No samples found: bcftools
[2020-11-28 16:22:30,690] multiqc [DEBUG ] No samples found: featureCounts
[2020-11-28 16:22:30,692] multiqc [DEBUG ] No samples found: fgbio
[2020-11-28 16:22:30,697] multiqc [DEBUG ] No samples found: dragen
[2020-11-28 16:22:30,700] multiqc [DEBUG ] No samples found: dedup
[2020-11-28 16:22:30,703] multiqc [DEBUG ] No samples found: damageprofiler
[2020-11-28 16:22:30,709] multiqc [DEBUG ] No samples found: biobambam2
[2020-11-28 16:22:30,711] multiqc [DEBUG ] No samples found: mtnucratio
[2020-11-28 16:22:30,714] multiqc [DEBUG ] No samples found: picard
[2020-11-28 16:22:30,717] multiqc [DEBUG ] No samples found: prokka
[2020-11-28 16:22:30,720] multiqc [DEBUG ] No samples found: samblaster
[2020-11-28 16:22:30,723] multiqc [DEBUG ] No samples found: samtools
[2020-11-28 16:22:30,726] multiqc [DEBUG ] No samples found: sexdeterrmine
[2020-11-28 16:22:30,729] multiqc [DEBUG ] No samples found: bamtools
[2020-11-28 16:22:30,731] multiqc [DEBUG ] No samples found: jellyfish
[2020-11-28 16:22:30,735] multiqc [DEBUG ] No samples found: vcftools
[2020-11-28 16:22:30,739] multiqc [DEBUG ] No samples found: longranger
[2020-11-28 16:22:30,742] multiqc [DEBUG ] No samples found: stacks
[2020-11-28 16:22:30,745] multiqc [DEBUG ] No samples found: varscan2
[2020-11-28 16:22:30,750] multiqc [DEBUG ] No samples found: bbmap
[2020-11-28 16:22:30,753] multiqc [DEBUG ] No samples found: bismark
[2020-11-28 16:22:30,756] multiqc [DEBUG ] No samples found: biscuit
[2020-11-28 16:22:30,759] multiqc [DEBUG ] No samples found: hicexplorer
[2020-11-28 16:22:30,762] multiqc [DEBUG ] No samples found: hicup
[2020-11-28 16:22:30,765] multiqc [DEBUG ] No samples found: hicpro
[2020-11-28 16:22:30,767] multiqc [DEBUG ] No samples found: salmon
[2020-11-28 16:22:30,770] multiqc [DEBUG ] No samples found: kallisto
[2020-11-28 16:22:30,772] multiqc [DEBUG ] No samples found: slamdunk
[2020-11-28 16:22:30,775] multiqc [DEBUG ] No samples found: star
[2020-11-28 16:22:30,777] multiqc [DEBUG ] No samples found: hisat2
[2020-11-28 16:22:30,780] multiqc [DEBUG ] No samples found: tophat
[2020-11-28 16:22:30,783] multiqc [DEBUG ] No samples found: bowtie2
[2020-11-28 16:22:30,786] multiqc [DEBUG ] No samples found: bowtie1
[2020-11-28 16:22:30,788] multiqc [DEBUG ] No samples found: snpsplit
[2020-11-28 16:22:30,791] multiqc [DEBUG ] No samples found: kat
[2020-11-28 16:22:30,794] multiqc [DEBUG ] No samples found: leehom
[2020-11-28 16:22:30,796] multiqc [DEBUG ] No samples found: adapterRemoval
[2020-11-28 16:22:30,798] multiqc [DEBUG ] No samples found: clipandmerge
[2020-11-28 16:22:30,801] multiqc [DEBUG ] No samples found: cutadapt
[2020-11-28 16:22:30,803] multiqc [DEBUG ] No samples found: flexbar
[2020-11-28 16:22:30,806] multiqc [DEBUG ] No samples found: kaiju
[2020-11-28 16:22:30,808] multiqc [DEBUG ] No samples found: kraken
[2020-11-28 16:22:30,811] multiqc [DEBUG ] No samples found: malt
[2020-11-28 16:22:30,813] multiqc [DEBUG ] No samples found: trimmomatic
[2020-11-28 16:22:30,816] multiqc [DEBUG ] No samples found: sickle
[2020-11-28 16:22:30,818] multiqc [DEBUG ] No samples found: skewer
[2020-11-28 16:22:30,820] multiqc [DEBUG ] No samples found: sortmerna
[2020-11-28 16:22:30,823] multiqc [DEBUG ] No samples found: biobloomtools
[2020-11-28 16:22:30,825] multiqc [DEBUG ] No samples found: fastq_screen
[2020-11-28 16:22:30,828] multiqc [DEBUG ] No samples found: afterqc
[2020-11-28 16:22:30,830] multiqc [DEBUG ] No samples found: fastp
[2020-11-28 16:22:30,845] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
[2020-11-28 16:22:30,896] multiqc [DEBUG ] No samples found: pycoqc
[2020-11-28 16:22:30,899] multiqc [DEBUG ] No samples found: minionqc
[2020-11-28 16:22:30,901] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2020-11-28 16:22:30,904] multiqc [DEBUG ] No samples found: clusterflow
[2020-11-28 16:22:30,906] multiqc [DEBUG ] No samples found: bcl2fastq
[2020-11-28 16:22:30,908] multiqc [DEBUG ] No samples found: interop
[2020-11-28 16:22:30,911] multiqc [DEBUG ] No samples found: ivar
[2020-11-28 16:22:30,914] multiqc [DEBUG ] No samples found: flash
[2020-11-28 16:22:30,916] multiqc [DEBUG ] No samples found: seqyclean
[2020-11-28 16:22:30,921] multiqc [INFO ] Compressing plot data
[2020-11-28 16:22:30,951] multiqc [INFO ] Report : multiqc_report.html
[2020-11-28 16:22:30,951] multiqc [INFO ] Data : multiqc_data
[2020-11-28 16:22:30,951] multiqc [DEBUG ] Moving data file from '/tmp/tmp2h0fqr8s/multiqc_data' to '/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/multiqc_data'
[2020-11-28 16:22:31,035] multiqc [INFO ] MultiQC complete

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tests/data/multiqc/multiqc_data/multiqc_data.json
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tests/data/multiqc/multiqc_data/multiqc_fastqc.txt
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Sample Filename File type Encoding Total Sequences Sequences flagged as poor quality Sequence length %GC total_deduplicated_percentage avg_sequence_length basic_statistics per_base_sequence_quality per_tile_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content
test_1 test_1.fastq.gz Conventional base calls Sanger / Illumina 1.9 10000.0 0.0 76.0 44.0 91.72 76.0 pass pass pass pass fail pass pass pass pass warn pass
test_2 test_2.fastq.gz Conventional base calls Sanger / Illumina 1.9 10000.0 0.0 76.0 44.0 91.63 76.0 pass pass pass pass fail pass pass pass pass warn pass

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tests/data/multiqc/multiqc_data/multiqc_general_stats.txt
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Sample 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
test_1 8.280000000000001 44.0 76.0 9.090909090909092 10000.0
test_2 8.370000000000005 44.0 76.0 9.090909090909092 10000.0

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tests/data/multiqc/multiqc_data/multiqc_sources.txt
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Module Section Sample Name Source
FastQC all_sections test_1 /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_1_fastqc.zip
FastQC all_sections test_2 /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_2_fastqc.zip

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tests/data/multiqc/multiqc_report.html
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tests/software/multiqc/test.yml
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- multiqc
files:
- path: output/test_multiqc/multiqc_report.html