Fixing MULTIQC module and adding tests (#1)

* fix multiqc process

* fix multiqc tests

* move multiqc test input data into tests/data/fastqc/ folder

Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation

* add multiqc github workflow

* remove unused file

* generalize multiqc input data

User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report

* update meta information
This commit is contained in:
Paolo Cozzi 2020-11-29 08:50:23 +01:00 committed by Abhinav Sharma
parent 2783913122
commit 835ac48565
21 changed files with 920 additions and 757 deletions

30
.github/workflows/multiqc.yml vendored Normal file
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@ -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

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@ -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
"""
}
}

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@ -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"

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../../../../tests/data/fastqc/test_1_fastqc.html

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../../../../tests/data/fastqc/test_1_fastqc.zip

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../../../../tests/data/fastqc/test_2_fastqc.html

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../../../../tests/data/fastqc/test_2_fastqc.zip

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@ -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()
}

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@ -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

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@ -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

View file

@ -2,26 +2,26 @@
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@ -133,7 +133,7 @@
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@ -540,8 +540,8 @@
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@ -749,8 +749,8 @@
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@ -2424,14 +2424,15 @@
"id": "fastqc_per_sequence_gc_content_plot",
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{
@ -2442,8 +2443,7 @@
"name": "Counts",
"ylab": "Count"
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@ -2819,8 +2819,8 @@
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@ -2918,11 +2918,13 @@
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},
"fastqc_adapter_content_plot": {
@ -3650,35 +3652,13 @@
],
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@ -3700,18 +3680,40 @@
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@ -3720,19 +3722,19 @@
}
},
"config_analysis_dir_abs": [
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View file

@ -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

View file

@ -1,3 +0,0 @@
Module Section Sample Name Source
FastQC all_sections test_2 /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_2_fastqc.zip
FastQC all_sections test_1 /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input/test_1_fastqc.zip

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