mirror of
https://github.com/MillironX/nf-core_modules.git
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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
Abhinav Sharma
parent
2783913122
commit
835ac48565
21 changed files with 920 additions and 757 deletions
30
.github/workflows/multiqc.yml
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.github/workflows/multiqc.yml
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name: multiqc
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on:
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push:
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paths:
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- software/multiqc/**
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- .github/workflows/multiqc.yml
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- tests
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pull_request:
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paths:
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- software/multiqc/**
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- .github/workflows/multiqc.yml
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- tests
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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run: |
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export NXF_VER="20.07.1"
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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# Test the module
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- run: nextflow run ./software/multiqc/test/ -profile docker
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@ -4,29 +4,29 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process FASTQC {
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tag "$meta.id"
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process MULTIQC {
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tag "multiqc"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: meta.id) }
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saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id:'') }
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conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
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container "quay.io/biocontainers/multiqc:1.9--py_1"
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input:
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tuple val(meta), path("*.html")
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path(generic_report)
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output:
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tuple val(meta), path("multiqc_data"), emit: dir
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tuple val(meta), path("*.html"), emit: html
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path("multiqc_data"), emit: dir
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path("multiqc_report.html"), emit: html
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
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"""
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multiqc --version | sed -e "s/version//g" > ${software}.version.txt
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multiqc .
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multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
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"""
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}
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}
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@ -1,20 +1,16 @@
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name: fastqc
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description: Run FastQC on sequenced reads
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name: MultiQC
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description: Aggregate results from bioinformatics analyses across many samples into a single report
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keywords:
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- quality control
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- qc
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- adapters
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- fastq
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- QC
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- bioinformatics tools
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- Beautiful stand-alone HTML report
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tools:
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- fastqc:
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- multiqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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MultiQC searches a given directory for analysis logs and compiles a HTML report.
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It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
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homepage: https://multiqc.info/
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documentation: https://multiqc.info/docs/
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params:
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- outdir:
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type: string
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@ -32,36 +28,23 @@ params:
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Run the module with Conda using the software specified
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via the `conda` directive
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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- generic_report:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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List of report, for example the html and zip output of FastQC
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- dir:
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type: dir
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description: MultiQC data dir
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pattern: "multiqc_data"
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- html:
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type: file
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description: FastQC report
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pattern: "*_{fastqc.html}"
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- zip:
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type: file
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description: FastQC report archive
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pattern: "*_{fastqc.zip}"
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description: MultiQC report file
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pattern: "multiqc_report.html"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@drpatelh"
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- "@grst"
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- "@ewels"
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- "@FelixKrueger"
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- "@abhi18av"
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- "@bunop"
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software/multiqc/test/input/test_1_fastqc.html
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software/multiqc/test/input/test_1_fastqc.html
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../../../../tests/data/fastqc/test_1_fastqc.html
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software/multiqc/test/input/test_1_fastqc.zip
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software/multiqc/test/input/test_1_fastqc.zip
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../../../../tests/data/fastqc/test_1_fastqc.zip
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software/multiqc/test/input/test_2_fastqc.html
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../../../../tests/data/fastqc/test_2_fastqc.html
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software/multiqc/test/input/test_2_fastqc.zip
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../../../../tests/data/fastqc/test_2_fastqc.zip
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@ -2,20 +2,24 @@
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nextflow.enable.dsl = 2
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include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { MULTIQC } from '../main.nf' addParams( options: [ publish_dir:'test_multi' ] )
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/*
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* Test with single-end data
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*/
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workflow test_single_end {
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workflow test_multi {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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input = [
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file("${baseDir}/input/test_1_fastqc.html", checkIfExists: true),
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file("${baseDir}/input/test_2_fastqc.html", checkIfExists: true),
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file("${baseDir}/input/test_1_fastqc.zip", checkIfExists: true),
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file("${baseDir}/input/test_2_fastqc.zip", checkIfExists: true)
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]
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FASTQC_SE ( input )
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MULTIQC ( input )
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}
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workflow {
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test_single_end()
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test_multi()
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}
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@ -1,105 +0,0 @@
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[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
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[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: /Users/eklavya/.multiqc_config.yaml
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[2020-11-23 18:25:23,742] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
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[2020-11-23 18:25:23,742] multiqc [DEBUG ] Command used: /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/
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[2020-11-23 18:25:25,158] multiqc [WARNING] MultiQC Version v1.9 now available!
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[2020-11-23 18:25:25,158] multiqc [INFO ] This is MultiQC v1.8
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[2020-11-23 18:25:25,158] multiqc [DEBUG ] Command : /Users/eklavya/.pyenv/versions/miniconda3-latest/bin/multiqc input/
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[2020-11-23 18:25:25,158] multiqc [DEBUG ] Working dir : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test
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[2020-11-23 18:25:25,158] multiqc [INFO ] Template : default
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[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)]
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[2020-11-23 18:25:25,159] multiqc [INFO ] Searching : /Users/eklavya/projects/code/ORG_nf_core/modules/software/multiqc/test/input
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[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
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[2020-11-23 18:25:25,159] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/zp/63677vtx23d_b2_nd7mm92040000gn/T/tmph8bg8w5g
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[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_1_fastqc.html
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[2020-11-23 18:25:25,251] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_2_fastqc.html
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[2020-11-23 18:25:25,624] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.1.1
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[2020-11-23 18:25:25,625] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.1.1
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[2020-11-23 18:25:25,626] multiqc [DEBUG ] No samples found: custom_content
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[2020-11-23 18:25:25,630] multiqc [DEBUG ] No samples found: conpair
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[2020-11-23 18:25:25,634] multiqc [DEBUG ] No samples found: peddy
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[2020-11-23 18:25:25,638] multiqc [DEBUG ] No samples found: methylQA
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[2020-11-23 18:25:25,642] multiqc [DEBUG ] No samples found: phantompeakqualtools
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[2020-11-23 18:25:25,647] multiqc [DEBUG ] No samples found: qualimap
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[2020-11-23 18:25:25,651] multiqc [DEBUG ] No samples found: preseq
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[2020-11-23 18:25:25,655] multiqc [DEBUG ] No samples found: quast
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[2020-11-23 18:25:25,659] multiqc [DEBUG ] No samples found: qorts
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[2020-11-23 18:25:25,663] multiqc [DEBUG ] No samples found: rna_seqc
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[2020-11-23 18:25:25,666] multiqc [DEBUG ] No samples found: rsem
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[2020-11-23 18:25:25,675] multiqc [DEBUG ] No samples found: rseqc
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[2020-11-23 18:25:25,679] multiqc [DEBUG ] No samples found: busco
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[2020-11-23 18:25:25,683] multiqc [DEBUG ] No samples found: goleft_indexcov
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[2020-11-23 18:25:25,687] multiqc [DEBUG ] No samples found: disambiguate
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[2020-11-23 18:25:25,691] multiqc [DEBUG ] No samples found: supernova
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[2020-11-23 18:25:25,700] multiqc [DEBUG ] No samples found: deeptools
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[2020-11-23 18:25:25,703] multiqc [DEBUG ] No samples found: sargasso
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[2020-11-23 18:25:25,707] multiqc [DEBUG ] No samples found: verifybamid
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[2020-11-23 18:25:25,711] multiqc [DEBUG ] No samples found: mirtrace
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[2020-11-23 18:25:25,715] multiqc [DEBUG ] No samples found: happy
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[2020-11-23 18:25:25,720] multiqc [DEBUG ] No samples found: homer
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[2020-11-23 18:25:25,723] multiqc [DEBUG ] No samples found: macs2
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[2020-11-23 18:25:25,727] multiqc [DEBUG ] No samples found: theta2
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[2020-11-23 18:25:25,731] multiqc [DEBUG ] No samples found: snpeff
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[2020-11-23 18:25:25,736] multiqc [DEBUG ] No samples found: gatk
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[2020-11-23 18:25:25,741] multiqc [DEBUG ] No samples found: htseq
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[2020-11-23 18:25:25,745] multiqc [DEBUG ] No samples found: bcftools
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[2020-11-23 18:25:25,750] multiqc [DEBUG ] No samples found: featureCounts
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[2020-11-23 18:25:25,754] multiqc [DEBUG ] No samples found: fgbio
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[2020-11-23 18:25:25,758] multiqc [DEBUG ] No samples found: dedup
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[2020-11-23 18:25:25,762] multiqc [DEBUG ] No samples found: damageprofiler
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[2020-11-23 18:25:25,774] multiqc [DEBUG ] No samples found: biobambam2
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[2020-11-23 18:25:25,778] multiqc [DEBUG ] No samples found: mtnucratio
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[2020-11-23 18:25:25,781] multiqc [DEBUG ] No samples found: picard
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[2020-11-23 18:25:25,785] multiqc [DEBUG ] No samples found: prokka
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[2020-11-23 18:25:25,789] multiqc [DEBUG ] No samples found: samblaster
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[2020-11-23 18:25:25,795] multiqc [DEBUG ] No samples found: samtools
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[2020-11-23 18:25:25,799] multiqc [DEBUG ] No samples found: sexdeterrmine
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[2020-11-23 18:25:25,803] multiqc [DEBUG ] No samples found: bamtools
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[2020-11-23 18:25:25,806] multiqc [DEBUG ] No samples found: jellyfish
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[2020-11-23 18:25:25,812] multiqc [DEBUG ] No samples found: vcftools
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[2020-11-23 18:25:25,816] multiqc [DEBUG ] No samples found: longranger
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[2020-11-23 18:25:25,820] multiqc [DEBUG ] No samples found: stacks
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[2020-11-23 18:25:25,830] multiqc [DEBUG ] No samples found: bbmap
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[2020-11-23 18:25:25,834] multiqc [DEBUG ] No samples found: bismark
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[2020-11-23 18:25:25,838] multiqc [DEBUG ] No samples found: biscuit
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[2020-11-23 18:25:25,842] multiqc [DEBUG ] No samples found: hicexplorer
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[2020-11-23 18:25:25,846] multiqc [DEBUG ] No samples found: hicup
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[2020-11-23 18:25:25,850] multiqc [DEBUG ] No samples found: hicpro
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[2020-11-23 18:25:25,853] multiqc [DEBUG ] No samples found: salmon
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[2020-11-23 18:25:25,857] multiqc [DEBUG ] No samples found: kallisto
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[2020-11-23 18:25:25,861] multiqc [DEBUG ] No samples found: slamdunk
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[2020-11-23 18:25:25,865] multiqc [DEBUG ] No samples found: star
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[2020-11-23 18:25:25,868] multiqc [DEBUG ] No samples found: hisat2
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[2020-11-23 18:25:25,872] multiqc [DEBUG ] No samples found: tophat
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[2020-11-23 18:25:25,875] multiqc [DEBUG ] No samples found: bowtie2
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[2020-11-23 18:25:25,879] multiqc [DEBUG ] No samples found: bowtie1
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[2020-11-23 18:25:25,883] multiqc [DEBUG ] No samples found: kat
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[2020-11-23 18:25:25,886] multiqc [DEBUG ] No samples found: leehom
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[2020-11-23 18:25:25,890] multiqc [DEBUG ] No samples found: adapterRemoval
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[2020-11-23 18:25:25,893] multiqc [DEBUG ] No samples found: clipandmerge
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[2020-11-23 18:25:25,897] multiqc [DEBUG ] No samples found: cutadapt
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[2020-11-23 18:25:25,901] multiqc [DEBUG ] No samples found: flexbar
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[2020-11-23 18:25:25,904] multiqc [DEBUG ] No samples found: trimmomatic
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[2020-11-23 18:25:25,908] multiqc [DEBUG ] No samples found: skewer
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[2020-11-23 18:25:25,912] multiqc [DEBUG ] No samples found: sortmerna
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[2020-11-23 18:25:25,915] multiqc [DEBUG ] No samples found: biobloomtools
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[2020-11-23 18:25:25,919] multiqc [DEBUG ] No samples found: fastq_screen
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[2020-11-23 18:25:25,922] multiqc [DEBUG ] No samples found: afterqc
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[2020-11-23 18:25:25,926] multiqc [DEBUG ] No samples found: fastp
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[2020-11-23 18:25:25,947] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
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[2020-11-23 18:25:26,023] multiqc [DEBUG ] No samples found: minionqc
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[2020-11-23 18:25:26,027] multiqc [DEBUG ] No samples found: mosdepth
|
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[2020-11-23 18:25:26,031] multiqc [DEBUG ] No samples found: clusterflow
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[2020-11-23 18:25:26,035] multiqc [DEBUG ] No samples found: bcl2fastq
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[2020-11-23 18:25:26,039] multiqc [DEBUG ] No samples found: interop
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[2020-11-23 18:25:26,043] multiqc [DEBUG ] No samples found: flash
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[2020-11-23 18:25:26,046] multiqc [DEBUG ] No samples found: seqyclean
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[2020-11-23 18:25:26,050] multiqc [INFO ] Compressing plot data
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[2020-11-23 18:25:26,086] multiqc [INFO ] Report : multiqc_report.html
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[2020-11-23 18:25:26,086] multiqc [INFO ] Data : multiqc_data
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[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'
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[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'
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[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
|
||||
127
software/multiqc/test/output/multiqc_data/multiqc.log
Normal file
127
software/multiqc/test/output/multiqc_data/multiqc.log
Normal file
|
|
@ -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
|
||||
|
|
@ -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": "<b>Base {point.x}</b>: {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": "<b>Phred {point.x}</b>: {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": "<b>{point.x}% GC</b>: {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": "<b>Base {point.x}</b>: {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": "<b>{point.x}</b>: {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"
|
||||
}
|
||||
|
|
@ -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
|
||||
|
|
@ -1 +0,0 @@
|
|||
Sample
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -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
|
||||
187
tests/data/fastqc/test_1_fastqc.html
Normal file
187
tests/data/fastqc/test_1_fastqc.html
Normal file
File diff suppressed because one or more lines are too long
BIN
tests/data/fastqc/test_1_fastqc.zip
Normal file
BIN
tests/data/fastqc/test_1_fastqc.zip
Normal file
Binary file not shown.
187
tests/data/fastqc/test_2_fastqc.html
Normal file
187
tests/data/fastqc/test_2_fastqc.html
Normal file
File diff suppressed because one or more lines are too long
BIN
tests/data/fastqc/test_2_fastqc.zip
Normal file
BIN
tests/data/fastqc/test_2_fastqc.zip
Normal file
Binary file not shown.
Loading…
Reference in a new issue