From 27b4b299761ed2eb0da4ad936c5d9ab0865f4d15 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Fri, 4 Dec 2020 20:15:48 +0530 Subject: [PATCH] Remove the extra data files --- .github/workflows/multiqc.yml | 3 +- tests/data/multiqc/multiqc_data/multiqc.log | 127 - .../multiqc/multiqc_data/multiqc_data.json | 3740 ---------- .../multiqc/multiqc_data/multiqc_fastqc.txt | 3 - .../multiqc_data/multiqc_general_stats.txt | 3 - .../multiqc/multiqc_data/multiqc_sources.txt | 3 - tests/data/multiqc/multiqc_report.html | 6269 ----------------- tests/software/multiqc/test.yml | 1 + 8 files changed, 3 insertions(+), 10146 deletions(-) delete mode 100644 tests/data/multiqc/multiqc_data/multiqc.log delete mode 100644 tests/data/multiqc/multiqc_data/multiqc_data.json delete mode 100644 tests/data/multiqc/multiqc_data/multiqc_fastqc.txt delete mode 100644 tests/data/multiqc/multiqc_data/multiqc_general_stats.txt delete mode 100644 tests/data/multiqc/multiqc_data/multiqc_sources.txt delete mode 100644 tests/data/multiqc/multiqc_report.html diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml index 1c45d5bd..37a830bd 100644 --- a/.github/workflows/multiqc.yml +++ b/.github/workflows/multiqc.yml @@ -34,4 +34,5 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow # Test the module - - run: pytest --tag multiqc --symlink --wt 2 \ No newline at end of file + - run: pytest --tag multiqc --symlink --wt 2 + diff --git a/tests/data/multiqc/multiqc_data/multiqc.log b/tests/data/multiqc/multiqc_data/multiqc.log deleted file mode 100644 index 99e190ac..00000000 --- a/tests/data/multiqc/multiqc_data/multiqc.log +++ /dev/null @@ -1,127 +0,0 @@ -[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 diff --git a/tests/data/multiqc/multiqc_data/multiqc_data.json b/tests/data/multiqc/multiqc_data/multiqc_data.json deleted file mode 100644 index af36fc89..00000000 --- a/tests/data/multiqc/multiqc_data/multiqc_data.json +++ /dev/null @@ -1,3740 +0,0 @@ -{ - "report_data_sources": { - "FastQC": { - "all_sections": { - "test_1": "/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_1_fastqc.zip", - "test_2": "/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52/test_2_fastqc.zip" - } - } - }, - "report_general_stats_data": [ - { - "test_1": { - "percent_gc": 44.0, - 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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 diff --git a/tests/data/multiqc/multiqc_data/multiqc_general_stats.txt b/tests/data/multiqc/multiqc_data/multiqc_general_stats.txt deleted file mode 100644 index 00541eff..00000000 --- a/tests/data/multiqc/multiqc_data/multiqc_general_stats.txt +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/tests/data/multiqc/multiqc_data/multiqc_sources.txt b/tests/data/multiqc/multiqc_data/multiqc_sources.txt deleted file mode 100644 index 1362141f..00000000 --- a/tests/data/multiqc/multiqc_data/multiqc_sources.txt +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/tests/data/multiqc/multiqc_report.html b/tests/data/multiqc/multiqc_report.html deleted file mode 100644 index d2f14276..00000000 --- a/tests/data/multiqc/multiqc_report.html +++ /dev/null @@ -1,6269 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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        MultiQC is published in Bioinformatics:

        -
        - MultiQC: Summarize analysis results for multiple tools and samples in a single report
        - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        - Bioinformatics (2016)
        - doi: 10.1093/bioinformatics/btw354
        - PMID: 27312411 -
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        - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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        Report - - generated on 2020-11-28, 16:22 - - - based on data in: - - /home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52

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        General Statistics

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        Sample Name% Dups% GCM Seqs
        test_1
        8.3%
        44%
        0.0
        test_2
        8.4%
        44%
        0.0
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        FastQC

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        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

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        - Sequence Counts - - - -

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        Sequence counts for each sample. Duplicate read counts are an estimate only.

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        This plot show the total number of reads, broken down into unique and duplicate -if possible (only more recent versions of FastQC give duplicate info).

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        You can read more about duplicate calculation in the -FastQC documentation. -A small part has been copied here for convenience:

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        Only sequences which first appear in the first 100,000 sequences -in each file are analysed. This should be enough to get a good impression -for the duplication levels in the whole file. Each sequence is tracked to -the end of the file to give a representative count of the overall duplication level.

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        The duplication detection requires an exact sequence match over the whole length of -the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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        - Sequence Quality Histograms - - - -

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        The mean quality value across each base position in the read.

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        To enable multiple samples to be plotted on the same graph, only the mean quality -scores are plotted (unlike the box plots seen in FastQC reports).

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        Taken from the FastQC help:

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        The y-axis on the graph shows the quality scores. The higher the score, the better -the base call. The background of the graph divides the y axis into very good quality -calls (green), calls of reasonable quality (orange), and calls of poor quality (red). -The quality of calls on most platforms will degrade as the run progresses, so it is -common to see base calls falling into the orange area towards the end of a read.

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        - Per Sequence Quality Scores - - - -

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        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

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        From the FastQC help:

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        The per sequence quality score report allows you to see if a subset of your -sequences have universally low quality values. It is often the case that a -subset of sequences will have universally poor quality, however these should -represent only a small percentage of the total sequences.

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        - Per Base Sequence Content - - - -

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        The proportion of each base position for which each of the four normal DNA bases has been called.

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        To enable multiple samples to be shown in a single plot, the base composition data -is shown as a heatmap. The colours represent the balance between the four bases: -an even distribution should give an even muddy brown colour. Hover over the plot -to see the percentage of the four bases under the cursor.

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        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

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        From the FastQC help:

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        Per Base Sequence Content plots out the proportion of each base position in a -file for which each of the four normal DNA bases has been called.

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        In a random library you would expect that there would be little to no difference -between the different bases of a sequence run, so the lines in this plot should -run parallel with each other. The relative amount of each base should reflect -the overall amount of these bases in your genome, but in any case they should -not be hugely imbalanced from each other.

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        It's worth noting that some types of library will always produce biased sequence -composition, normally at the start of the read. Libraries produced by priming -using random hexamers (including nearly all RNA-Seq libraries) and those which -were fragmented using transposases inherit an intrinsic bias in the positions -at which reads start. This bias does not concern an absolute sequence, but instead -provides enrichement of a number of different K-mers at the 5' end of the reads. -Whilst this is a true technical bias, it isn't something which can be corrected -by trimming and in most cases doesn't seem to adversely affect the downstream -analysis.

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        - Per Sequence GC Content - - - -

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        The average GC content of reads. Normal random library typically have a - roughly normal distribution of GC content.

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        From the FastQC help:

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        This module measures the GC content across the whole length of each sequence -in a file and compares it to a modelled normal distribution of GC content.

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        In a normal random library you would expect to see a roughly normal distribution -of GC content where the central peak corresponds to the overall GC content of -the underlying genome. Since we don't know the the GC content of the genome the -modal GC content is calculated from the observed data and used to build a -reference distribution.

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        An unusually shaped distribution could indicate a contaminated library or -some other kinds of biased subset. A normal distribution which is shifted -indicates some systematic bias which is independent of base position. If there -is a systematic bias which creates a shifted normal distribution then this won't -be flagged as an error by the module since it doesn't know what your genome's -GC content should be.

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        - Per Base N Content - - - -

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        The percentage of base calls at each position for which an N was called.

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        From the FastQC help:

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        If a sequencer is unable to make a base call with sufficient confidence then it will -normally substitute an N rather than a conventional base call. This graph shows the -percentage of base calls at each position for which an N was called.

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        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially -nearer the end of a sequence. However, if this proportion rises above a few percent -it suggests that the analysis pipeline was unable to interpret the data well enough to -make valid base calls.

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        - Sequence Length Distribution - -

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        All samples have sequences of a single length (76bp).
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        - Sequence Duplication Levels - - - -

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        The relative level of duplication found for every sequence.

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        From the FastQC Help:

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        In a diverse library most sequences will occur only once in the final set. -A low level of duplication may indicate a very high level of coverage of the -target sequence, but a high level of duplication is more likely to indicate -some kind of enrichment bias (eg PCR over amplification). This graph shows -the degree of duplication for every sequence in a library: the relative -number of sequences with different degrees of duplication.

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        Only sequences which first appear in the first 100,000 sequences -in each file are analysed. This should be enough to get a good impression -for the duplication levels in the whole file. Each sequence is tracked to -the end of the file to give a representative count of the overall duplication level.

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        The duplication detection requires an exact sequence match over the whole length of -the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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        In a properly diverse library most sequences should fall into the far left of the -plot in both the red and blue lines. A general level of enrichment, indicating broad -oversequencing in the library will tend to flatten the lines, lowering the low end -and generally raising other categories. More specific enrichments of subsets, or -the presence of low complexity contaminants will tend to produce spikes towards the -right of the plot.

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        - Overrepresented sequences - - - -

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        The total amount of overrepresented sequences found in each library.

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        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be -possible to show this for all samples in a MultiQC report, so instead this plot shows -the number of sequences categorized as over represented.

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        Sometimes, a single sequence may account for a large number of reads in a dataset. -To show this, the bars are split into two: the first shows the overrepresented reads -that come from the single most common sequence. The second shows the total count -from all remaining overrepresented sequences.

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        From the FastQC Help:

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        A normal high-throughput library will contain a diverse set of sequences, with no -individual sequence making up a tiny fraction of the whole. Finding that a single -sequence is very overrepresented in the set either means that it is highly biologically -significant, or indicates that the library is contaminated, or not as diverse as you expected.

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        FastQC lists all of the sequences which make up more than 0.1% of the total. -To conserve memory only sequences which appear in the first 100,000 sequences are tracked -to the end of the file. It is therefore possible that a sequence which is overrepresented -but doesn't appear at the start of the file for some reason could be missed by this module.

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        2 samples had less than 1% of reads made up of overrepresented sequences
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        - Adapter Content - - - -

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        The cumulative percentage count of the proportion of your - library which has seen each of the adapter sequences at each position.

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        Note that only samples with ≥ 0.1% adapter contamination are shown.

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        There may be several lines per sample, as one is shown for each adapter -detected in the file.

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        From the FastQC Help:

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        The plot shows a cumulative percentage count of the proportion -of your library which has seen each of the adapter sequences at each position. -Once a sequence has been seen in a read it is counted as being present -right through to the end of the read so the percentages you see will only -increase as the read length goes on.

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        - Status Checks - - - -

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        Status for each FastQC section showing whether results seem entirely normal (green), -slightly abnormal (orange) or very unusual (red).

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        FastQC assigns a status for each section of the report. -These give a quick evaluation of whether the results of the analysis seem -entirely normal (green), slightly abnormal (orange) or very unusual (red).

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        It is important to stress that although the analysis results appear to give a pass/fail result, -these evaluations must be taken in the context of what you expect from your library. -A 'normal' sample as far as FastQC is concerned is random and diverse. -Some experiments may be expected to produce libraries which are biased in particular ways. -You should treat the summary evaluations therefore as pointers to where you should concentrate -your attention and understand why your library may not look random and diverse.

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        Specific guidance on how to interpret the output of each module can be found in the relevant -report section, or in the FastQC help.

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        In this heatmap, we summarise all of these into a single heatmap for a quick overview. -Note that not all FastQC sections have plots in MultiQC reports, but all status checks -are shown in this heatmap.

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        - - - - - MultiQC v1.9 - - - Written by Phil Ewels, - available on GitHub. -

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        - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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        - - - - - - - - - - - - - - diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml index 6b1a198b..7fc6d7a3 100644 --- a/tests/software/multiqc/test.yml +++ b/tests/software/multiqc/test.yml @@ -4,3 +4,4 @@ - multiqc files: - path: output/test_multiqc/multiqc_report.html +