diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml new file mode 100644 index 00000000..542d3317 --- /dev/null +++ b/.github/workflows/multiqc.yml @@ -0,0 +1,30 @@ +name: multiqc +on: + push: + paths: + - software/multiqc/** + - .github/workflows/multiqc.yml + - tests + pull_request: + paths: + - software/multiqc/** + - .github/workflows/multiqc.yml + - tests + +jobs: + ci_test: + runs-on: ubuntu-latest + env: + NXF_ANSI_LOG: false + steps: + + - uses: actions/checkout@v2 + + - name: Install Nextflow + run: | + export NXF_VER="20.07.1" + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + # Test the module + - run: nextflow run ./software/multiqc/test/ -profile docker diff --git a/software/multiqc/main.nf b/software/multiqc/main.nf index 0fef306b..ddf4ea3e 100644 --- a/software/multiqc/main.nf +++ b/software/multiqc/main.nf @@ -4,29 +4,29 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) -process FASTQC { - tag "$meta.id" +process MULTIQC { + tag "multiqc" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: meta.id) } + saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id:'') } conda(params.enable_conda ? "bioconda::multiqc=1.9" : null) container "quay.io/biocontainers/multiqc:1.9--py_1" input: - tuple val(meta), path("*.html") + path(generic_report) output: - tuple val(meta), path("multiqc_data"), emit: dir - tuple val(meta), path("*.html"), emit: html + path("multiqc_data"), emit: dir + path("multiqc_report.html"), emit: html path "*.version.txt", emit: version script: def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" - """ - multiqc --version | sed -e "s/version//g" > ${software}.version.txt - """ - } + + """ + multiqc . + multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt + """ } diff --git a/software/multiqc/meta.yml b/software/multiqc/meta.yml index 337fc372..9d2c2dde 100644 --- a/software/multiqc/meta.yml +++ b/software/multiqc/meta.yml @@ -1,20 +1,16 @@ -name: fastqc -description: Run FastQC on sequenced reads +name: MultiQC +description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - - quality control - - qc - - adapters - - fastq + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report tools: - - fastqc: + - multiqc: description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ params: - outdir: type: string @@ -32,36 +28,23 @@ params: Run the module with Conda using the software specified via the `conda` directive input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: + - generic_report: type: file description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + List of report, for example the html and zip output of FastQC output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - dir: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" - html: type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + description: MultiQC report file + pattern: "multiqc_report.html" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@abhi18av" + - "@bunop" diff --git a/software/multiqc/test/input/test_1_fastqc.html b/software/multiqc/test/input/test_1_fastqc.html deleted file mode 100644 index e33dddbe..00000000 --- a/software/multiqc/test/input/test_1_fastqc.html +++ /dev/null @@ -1,187 +0,0 @@ -test_1.fastq.gz FastQC Report
FastQCFastQC Report
Fri 7 Aug 2020
test_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
Filenametest_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences10000
Sequences flagged as poor quality0
Sequence length76
%GC44

[OK]Per base sequence quality

Per base quality graph

[OK]Per tile sequence quality

Per tile quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[OK]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT230.22999999999999998No Hit
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT160.16No Hit
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT150.15No Hit

[OK]Adapter Content

Adapter graph

Produced by FastQC (version 0.11.9)
\ No newline at end of file diff --git a/software/multiqc/test/input/test_1_fastqc.html b/software/multiqc/test/input/test_1_fastqc.html new file mode 120000 index 00000000..c045f6f5 --- /dev/null +++ b/software/multiqc/test/input/test_1_fastqc.html @@ -0,0 +1 @@ +../../../../tests/data/fastqc/test_1_fastqc.html \ No newline at end of file diff --git a/software/multiqc/test/input/test_1_fastqc.zip b/software/multiqc/test/input/test_1_fastqc.zip deleted file mode 100644 index 82b12818..00000000 Binary files a/software/multiqc/test/input/test_1_fastqc.zip and /dev/null differ diff --git a/software/multiqc/test/input/test_1_fastqc.zip b/software/multiqc/test/input/test_1_fastqc.zip new file mode 120000 index 00000000..b7a4f15d --- /dev/null +++ b/software/multiqc/test/input/test_1_fastqc.zip @@ -0,0 +1 @@ +../../../../tests/data/fastqc/test_1_fastqc.zip \ No newline at end of file diff --git a/software/multiqc/test/input/test_2_fastqc.html b/software/multiqc/test/input/test_2_fastqc.html deleted file mode 100644 index 5fb48f29..00000000 --- a/software/multiqc/test/input/test_2_fastqc.html +++ /dev/null @@ -1,187 +0,0 @@ -test_2.fastq.gz FastQC Report
FastQCFastQC Report
Fri 7 Aug 2020
test_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
Filenametest_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences10000
Sequences flagged as poor quality0
Sequence length76
%GC44

[OK]Per base sequence quality

Per base quality graph

[OK]Per tile sequence quality

Per tile quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[OK]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT190.19No Hit

[OK]Adapter Content

Adapter graph

Produced by FastQC (version 0.11.9)
\ No newline at end of file diff --git a/software/multiqc/test/input/test_2_fastqc.html b/software/multiqc/test/input/test_2_fastqc.html new file mode 120000 index 00000000..75278d27 --- /dev/null +++ b/software/multiqc/test/input/test_2_fastqc.html @@ -0,0 +1 @@ +../../../../tests/data/fastqc/test_2_fastqc.html \ No newline at end of file diff --git a/software/multiqc/test/input/test_2_fastqc.zip b/software/multiqc/test/input/test_2_fastqc.zip deleted file mode 100644 index b8741db9..00000000 Binary files a/software/multiqc/test/input/test_2_fastqc.zip and /dev/null differ diff --git a/software/multiqc/test/input/test_2_fastqc.zip b/software/multiqc/test/input/test_2_fastqc.zip new file mode 120000 index 00000000..3bf10898 --- /dev/null +++ b/software/multiqc/test/input/test_2_fastqc.zip @@ -0,0 +1 @@ +../../../../tests/data/fastqc/test_2_fastqc.zip \ No newline at end of file diff --git a/software/multiqc/test/main.nf b/software/multiqc/test/main.nf index a10ac986..60c7e1a0 100755 --- a/software/multiqc/test/main.nf +++ b/software/multiqc/test/main.nf @@ -2,20 +2,24 @@ nextflow.enable.dsl = 2 -include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] ) +include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_multi' ] ) /* * Test with single-end data */ -workflow test_single_end { +workflow test_multi { def input = [] - input = [ [ id:'test', single_end:true ], // meta map - [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ] + input = [ + file("${baseDir}/input/test_1_fastqc.html", checkIfExists: true), + file("${baseDir}/input/test_2_fastqc.html", checkIfExists: true), + file("${baseDir}/input/test_1_fastqc.zip", checkIfExists: true), + file("${baseDir}/input/test_2_fastqc.zip", checkIfExists: true) + ] - FASTQC_SE ( input ) + MULTIQC ( input ) } workflow { - test_single_end() + test_multi() } diff --git a/software/multiqc/test/output/multiqc.log b/software/multiqc/test/output/multiqc.log deleted file mode 100644 index a0ac427b..00000000 --- a/software/multiqc/test/output/multiqc.log +++ /dev/null @@ -1,105 +0,0 @@ -[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: /Users/eklavya/.pyenv/versions/miniconda3-latest/lib/python3.7/site-packages/multiqc_config.yaml -[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: /Users/eklavya/.multiqc_config.yaml -[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2020-11-23 18:25:23,742] multiqc [DEBUG ] Command used: /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/ -[2020-11-23 18:25:25,158] multiqc [WARNING] MultiQC Version v1.9 now available! -[2020-11-23 18:25:25,158] multiqc [INFO ] This is MultiQC v1.8 -[2020-11-23 18:25:25,158] multiqc [DEBUG ] Command : /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/ -[2020-11-23 18:25:25,158] multiqc [DEBUG ] Working dir : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test -[2020-11-23 18:25:25,158] multiqc [INFO ] Template : default -[2020-11-23 18:25:25,158] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 16:54:48) [Clang 4.0.1 (tags/RELEASE_401/final)] -[2020-11-23 18:25:25,159] multiqc [INFO ] Searching : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input -[2020-11-23 18:25:25,159] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean -[2020-11-23 18:25:25,159] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g -[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_1_fastqc.html -[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_2_fastqc.html -[2020-11-23 18:25:25,624] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.1.1 -[2020-11-23 18:25:25,625] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.1.1 -[2020-11-23 18:25:25,626] multiqc [DEBUG ] No samples found: custom_content -[2020-11-23 18:25:25,630] multiqc [DEBUG ] No samples found: conpair -[2020-11-23 18:25:25,634] multiqc [DEBUG ] No samples found: peddy -[2020-11-23 18:25:25,638] multiqc [DEBUG ] No samples found: methylQA -[2020-11-23 18:25:25,642] multiqc [DEBUG ] No samples found: phantompeakqualtools -[2020-11-23 18:25:25,647] multiqc [DEBUG ] No samples found: qualimap -[2020-11-23 18:25:25,651] multiqc [DEBUG ] No samples found: preseq -[2020-11-23 18:25:25,655] multiqc [DEBUG ] No samples found: quast -[2020-11-23 18:25:25,659] multiqc [DEBUG ] No samples found: qorts -[2020-11-23 18:25:25,663] multiqc [DEBUG ] No samples found: rna_seqc -[2020-11-23 18:25:25,666] multiqc [DEBUG ] No samples found: rsem -[2020-11-23 18:25:25,675] multiqc [DEBUG ] No samples found: rseqc -[2020-11-23 18:25:25,679] multiqc [DEBUG ] No samples found: busco -[2020-11-23 18:25:25,683] multiqc [DEBUG ] No samples found: goleft_indexcov -[2020-11-23 18:25:25,687] multiqc [DEBUG ] No samples found: disambiguate -[2020-11-23 18:25:25,691] multiqc [DEBUG ] No samples found: supernova -[2020-11-23 18:25:25,700] multiqc [DEBUG ] No samples found: deeptools -[2020-11-23 18:25:25,703] multiqc [DEBUG ] No samples found: sargasso -[2020-11-23 18:25:25,707] multiqc [DEBUG ] No samples found: verifybamid -[2020-11-23 18:25:25,711] multiqc [DEBUG ] No samples found: mirtrace -[2020-11-23 18:25:25,715] multiqc [DEBUG ] No samples found: happy -[2020-11-23 18:25:25,720] multiqc [DEBUG ] No samples found: homer -[2020-11-23 18:25:25,723] multiqc [DEBUG ] No samples found: macs2 -[2020-11-23 18:25:25,727] multiqc [DEBUG ] No samples found: theta2 -[2020-11-23 18:25:25,731] multiqc [DEBUG ] No samples found: snpeff -[2020-11-23 18:25:25,736] multiqc [DEBUG ] No samples found: gatk -[2020-11-23 18:25:25,741] multiqc [DEBUG ] No samples found: htseq -[2020-11-23 18:25:25,745] multiqc [DEBUG ] No samples found: bcftools -[2020-11-23 18:25:25,750] multiqc [DEBUG ] No samples found: featureCounts -[2020-11-23 18:25:25,754] multiqc [DEBUG ] No samples found: fgbio -[2020-11-23 18:25:25,758] multiqc [DEBUG ] No samples found: dedup -[2020-11-23 18:25:25,762] multiqc [DEBUG ] No samples found: damageprofiler -[2020-11-23 18:25:25,774] multiqc [DEBUG ] No samples found: biobambam2 -[2020-11-23 18:25:25,778] multiqc [DEBUG ] No samples found: mtnucratio -[2020-11-23 18:25:25,781] multiqc [DEBUG ] No samples found: picard -[2020-11-23 18:25:25,785] multiqc [DEBUG ] No samples found: prokka -[2020-11-23 18:25:25,789] multiqc [DEBUG ] No samples found: samblaster -[2020-11-23 18:25:25,795] multiqc [DEBUG ] No samples found: samtools -[2020-11-23 18:25:25,799] multiqc [DEBUG ] No samples found: sexdeterrmine -[2020-11-23 18:25:25,803] multiqc [DEBUG ] No samples found: bamtools -[2020-11-23 18:25:25,806] multiqc [DEBUG ] No samples found: jellyfish -[2020-11-23 18:25:25,812] multiqc [DEBUG ] No samples found: vcftools -[2020-11-23 18:25:25,816] multiqc [DEBUG ] No samples found: longranger -[2020-11-23 18:25:25,820] multiqc [DEBUG ] No samples found: stacks -[2020-11-23 18:25:25,830] multiqc [DEBUG ] No samples found: bbmap -[2020-11-23 18:25:25,834] multiqc [DEBUG ] No samples found: bismark -[2020-11-23 18:25:25,838] multiqc [DEBUG ] No samples found: biscuit -[2020-11-23 18:25:25,842] multiqc [DEBUG ] No samples found: hicexplorer -[2020-11-23 18:25:25,846] multiqc [DEBUG ] No samples found: hicup -[2020-11-23 18:25:25,850] multiqc [DEBUG ] No samples found: hicpro -[2020-11-23 18:25:25,853] multiqc [DEBUG ] No samples found: salmon -[2020-11-23 18:25:25,857] multiqc [DEBUG ] No samples found: kallisto -[2020-11-23 18:25:25,861] multiqc [DEBUG ] No samples found: slamdunk -[2020-11-23 18:25:25,865] multiqc [DEBUG ] No samples found: star -[2020-11-23 18:25:25,868] multiqc [DEBUG ] No samples found: hisat2 -[2020-11-23 18:25:25,872] multiqc [DEBUG ] No samples found: tophat -[2020-11-23 18:25:25,875] multiqc [DEBUG ] No samples found: bowtie2 -[2020-11-23 18:25:25,879] multiqc [DEBUG ] No samples found: bowtie1 -[2020-11-23 18:25:25,883] multiqc [DEBUG ] No samples found: kat -[2020-11-23 18:25:25,886] multiqc [DEBUG ] No samples found: leehom -[2020-11-23 18:25:25,890] multiqc [DEBUG ] No samples found: adapterRemoval -[2020-11-23 18:25:25,893] multiqc [DEBUG ] No samples found: clipandmerge -[2020-11-23 18:25:25,897] multiqc [DEBUG ] No samples found: cutadapt -[2020-11-23 18:25:25,901] multiqc [DEBUG ] No samples found: flexbar -[2020-11-23 18:25:25,904] multiqc [DEBUG ] No samples found: trimmomatic -[2020-11-23 18:25:25,908] multiqc [DEBUG ] No samples found: skewer -[2020-11-23 18:25:25,912] multiqc [DEBUG ] No samples found: sortmerna -[2020-11-23 18:25:25,915] multiqc [DEBUG ] No samples found: biobloomtools -[2020-11-23 18:25:25,919] multiqc [DEBUG ] No samples found: fastq_screen -[2020-11-23 18:25:25,922] multiqc [DEBUG ] No samples found: afterqc -[2020-11-23 18:25:25,926] multiqc [DEBUG ] No samples found: fastp -[2020-11-23 18:25:25,947] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports -[2020-11-23 18:25:26,023] multiqc [DEBUG ] No samples found: minionqc -[2020-11-23 18:25:26,027] multiqc [DEBUG ] No samples found: mosdepth -[2020-11-23 18:25:26,031] multiqc [DEBUG ] No samples found: clusterflow -[2020-11-23 18:25:26,035] multiqc [DEBUG ] No samples found: bcl2fastq -[2020-11-23 18:25:26,039] multiqc [DEBUG ] No samples found: interop -[2020-11-23 18:25:26,043] multiqc [DEBUG ] No samples found: flash -[2020-11-23 18:25:26,046] multiqc [DEBUG ] No samples found: seqyclean -[2020-11-23 18:25:26,050] multiqc [INFO ] Compressing plot data -[2020-11-23 18:25:26,086] multiqc [INFO ] Report : multiqc_report.html -[2020-11-23 18:25:26,086] multiqc [INFO ] Data : multiqc_data -[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_fastqc.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data' -[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data' -[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_general_stats.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data' -[2020-11-23 18:25:26,087] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_sources.txt' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data' -[2020-11-23 18:25:26,088] multiqc [DEBUG ] Moving data file from '/var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g/multiqc_data/multiqc_data.json' to '/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/multiqc_data' -[2020-11-23 18:25:26,231] multiqc [INFO ] MultiQC complete diff --git a/software/multiqc/test/output/multiqc_data/multiqc.log b/software/multiqc/test/output/multiqc_data/multiqc.log new file mode 100644 index 00000000..99e190ac --- /dev/null +++ b/software/multiqc/test/output/multiqc_data/multiqc.log @@ -0,0 +1,127 @@ +[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/software/multiqc/test/output/multiqc_data.json b/software/multiqc/test/output/multiqc_data/multiqc_data.json similarity index 98% rename from software/multiqc/test/output/multiqc_data.json rename to software/multiqc/test/output/multiqc_data/multiqc_data.json index f6789e80..af36fc89 100644 --- a/software/multiqc/test/output/multiqc_data.json +++ b/software/multiqc/test/output/multiqc_data/multiqc_data.json @@ -2,26 +2,26 @@ "report_data_sources": { "FastQC": { "all_sections": { - "test_2": "/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_2_fastqc.zip", - "test_1": "/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_1_fastqc.zip" + "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_2": { - "percent_gc": 44.0, - "avg_sequence_length": 76.0, - "total_sequences": 10000.0, - "percent_duplicates": 8.370000000000005, - "percent_fails": 9.090909090909092 - }, "test_1": { "percent_gc": 44.0, "avg_sequence_length": 76.0, "total_sequences": 10000.0, "percent_duplicates": 8.280000000000001, "percent_fails": 9.090909090909092 + }, + "test_2": { + "percent_gc": 44.0, + "avg_sequence_length": 76.0, + "total_sequences": 10000.0, + "percent_duplicates": 8.370000000000005, + "percent_fails": 9.090909090909092 } } ], @@ -133,7 +133,7 @@ } } ], - "report_multiqc_command": "/Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/", + "report_multiqc_command": "/usr/local/bin/multiqc .", "report_plot_data": { "fastqc_sequence_counts_plot": { "plot_type": "bar_graph", @@ -540,8 +540,8 @@ "xDecimals": false, "tt_label": "Base {point.x}: {point.y:.2f}", "colors": { - "test_2": "#5cb85c", - "test_1": "#5cb85c" + "test_1": "#5cb85c", + "test_2": "#5cb85c" }, "yPlotBands": [ { @@ -749,8 +749,8 @@ "xmin": 0, "xDecimals": false, "colors": { - "test_2": "#5cb85c", - "test_1": "#5cb85c" + "test_1": "#5cb85c", + "test_2": "#5cb85c" }, "tt_label": "Phred {point.x}: {point.y} reads", "xPlotBands": [ @@ -2424,14 +2424,15 @@ "id": "fastqc_per_sequence_gc_content_plot", "title": "FastQC: Per Sequence GC Content", "xlab": "% GC", + "ylab": "Percentage", "ymin": 0, "xmax": 100, "xmin": 0, "yDecimals": false, "tt_label": "{point.x}% GC: {point.y}", "colors": { - "test_2": "#5cb85c", - "test_1": "#5cb85c" + "test_1": "#5cb85c", + "test_2": "#5cb85c" }, "data_labels": [ { @@ -2442,8 +2443,7 @@ "name": "Counts", "ylab": "Count" } - ], - "ylab": "Percentage" + ] } }, "fastqc_per_base_n_content_plot": { @@ -2819,8 +2819,8 @@ "xmin": 0, "xDecimals": false, "colors": { - "test_2": "#5cb85c", - "test_1": "#5cb85c" + "test_1": "#5cb85c", + "test_2": "#5cb85c" }, "tt_label": "Base {point.x}: {point.y:.2f}%", "yPlotBands": [ @@ -2918,11 +2918,13 @@ "ymax": 100, "ymin": 0, "yMinTickInterval": 0.1, + "yLabelFormat": "{value:.0f}%", "colors": { - "test_2": "#5cb85c", - "test_1": "#5cb85c" + "test_1": "#5cb85c", + "test_2": "#5cb85c" }, - "tt_label": "{point.x}: {point.y:.1f}%" + "tt_decimals": 2, + "tt_suffix": "%" } }, "fastqc_adapter_content_plot": { @@ -3650,35 +3652,13 @@ ], "decimalPlaces": 1, "legend": false, - "datalabels": false + "datalabels": false, + "xcats_samples": false } } }, "report_saved_raw_data": { - "multiqc_qualimap_bamqc_genome_results": {}, "multiqc_fastqc": { - "test_2": { - "Filename": "test_2.fastq.gz", - "File type": "Conventional base calls", - "Encoding": "Sanger / Illumina 1.9", - "Total Sequences": 10000.0, - "Sequences flagged as poor quality": 0.0, - "Sequence length": 76.0, - "%GC": 44.0, - "total_deduplicated_percentage": 91.63, - "avg_sequence_length": 76.0, - "basic_statistics": "pass", - "per_base_sequence_quality": "pass", - "per_tile_sequence_quality": "pass", - "per_sequence_quality_scores": "pass", - "per_base_sequence_content": "fail", - "per_sequence_gc_content": "pass", - "per_base_n_content": "pass", - "sequence_length_distribution": "pass", - "sequence_duplication_levels": "pass", - "overrepresented_sequences": "warn", - "adapter_content": "pass" - }, "test_1": { "Filename": "test_1.fastq.gz", "File type": "Conventional base calls", @@ -3700,18 +3680,40 @@ "sequence_duplication_levels": "pass", "overrepresented_sequences": "warn", "adapter_content": "pass" + }, + "test_2": { + "Filename": "test_2.fastq.gz", + "File type": "Conventional base calls", + "Encoding": "Sanger / Illumina 1.9", + "Total Sequences": 10000.0, + "Sequences flagged as poor quality": 0.0, + "Sequence length": 76.0, + "%GC": 44.0, + "total_deduplicated_percentage": 91.63, + "avg_sequence_length": 76.0, + "basic_statistics": "pass", + "per_base_sequence_quality": "pass", + "per_tile_sequence_quality": "pass", + "per_sequence_quality_scores": "pass", + "per_base_sequence_content": "fail", + "per_sequence_gc_content": "pass", + "per_base_n_content": "pass", + "sequence_length_distribution": "pass", + "sequence_duplication_levels": "pass", + "overrepresented_sequences": "warn", + "adapter_content": "pass" } }, "multiqc_general_stats": { - "test_2": { - "FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.370000000000005, + "test_1": { + "FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.280000000000001, "FastQC_mqc-generalstats-fastqc-percent_gc": 44.0, "FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0, "FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092, "FastQC_mqc-generalstats-fastqc-total_sequences": 10000.0 }, - "test_1": { - "FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.280000000000001, + "test_2": { + "FastQC_mqc-generalstats-fastqc-percent_duplicates": 8.370000000000005, "FastQC_mqc-generalstats-fastqc-percent_gc": 44.0, "FastQC_mqc-generalstats-fastqc-avg_sequence_length": 76.0, "FastQC_mqc-generalstats-fastqc-percent_fails": 9.090909090909092, @@ -3720,19 +3722,19 @@ } }, "config_analysis_dir_abs": [ - "/Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input" + "/home/paolo/Projects/NEXTFLOWetude/nf-core-modules/work/cc/e69df4c4d3d33e79fbb670c7f14b52" ], "config_analysis_dir": [ - "input/" + "." ], - "config_creation_date": "2020-11-23, 18:25", + "config_creation_date": "2020-11-28, 16:22", "config_git_hash": null, "config_intro_text": null, "config_report_comment": null, "config_report_header_info": null, - "config_script_path": "/Users/eklavya/.pyenv/versions/miniconda3-latest/lib/python3.7/site-packages/multiqc/utils", - "config_short_version": "1.8", + "config_script_path": "/usr/local/lib/python3.8/site-packages/multiqc/utils", + "config_short_version": "1.9", "config_subtitle": null, "config_title": null, - "config_version": "1.8" + "config_version": "1.9" } diff --git a/software/multiqc/test/output/multiqc_fastqc.txt b/software/multiqc/test/output/multiqc_data/multiqc_fastqc.txt similarity index 100% rename from software/multiqc/test/output/multiqc_fastqc.txt rename to software/multiqc/test/output/multiqc_data/multiqc_fastqc.txt diff --git a/software/multiqc/test/output/multiqc_general_stats.txt b/software/multiqc/test/output/multiqc_data/multiqc_general_stats.txt similarity index 100% rename from software/multiqc/test/output/multiqc_general_stats.txt rename to software/multiqc/test/output/multiqc_data/multiqc_general_stats.txt diff --git a/software/multiqc/test/output/multiqc_data/multiqc_sources.txt b/software/multiqc/test/output/multiqc_data/multiqc_sources.txt new file mode 100644 index 00000000..1362141f --- /dev/null +++ b/software/multiqc/test/output/multiqc_data/multiqc_sources.txt @@ -0,0 +1,3 @@ +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/software/multiqc/test/output/multiqc_qualimap_bamqc_genome_results.txt b/software/multiqc/test/output/multiqc_qualimap_bamqc_genome_results.txt deleted file mode 100644 index 03a05ce7..00000000 --- a/software/multiqc/test/output/multiqc_qualimap_bamqc_genome_results.txt +++ /dev/null @@ -1 +0,0 @@ -Sample diff --git a/software/multiqc/test/multiqc_report.html b/software/multiqc/test/output/multiqc_report.html similarity index 98% rename from software/multiqc/test/multiqc_report.html rename to software/multiqc/test/output/multiqc_report.html index 3756d2f7..d2f14276 100644 --- a/software/multiqc/test/multiqc_report.html +++ b/software/multiqc/test/output/multiqc_report.html @@ -23,9 +23,9 @@ http://multiqc.info MultiQC Report - + - +

About MultiQC

-

This report was generated using MultiQC, version 1.8

+

This report was generated using MultiQC, version 1.9

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and @@ -5417,14 +5526,26 @@ function findPos(obj) {

+
-

Report generated on 2020-11-23, 18:25 based on data in: - /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input +

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

+
+ + + +