mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
initial attempt for multiqc module
This commit is contained in:
Abhinav Sharma
parent
e02f0de514
commit
2783913122
16 changed files with 10574 additions and 0 deletions
59
software/multiqc/functions.nf
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59
software/multiqc/functions.nf
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/*
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* -----------------------------------------------------
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* Utility functions used in nf-core DSL2 module files
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* -----------------------------------------------------
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*/
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/*
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* Extract name of software tool from process name using $task.process
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*/
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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/*
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* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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*/
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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/*
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* Tidy up and join elements of a list to return a path string
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*/
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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/*
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* Function to save/publish module results
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*/
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def saveFiles(Map args) {
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if (!args.filename.endsWith('.version.txt')) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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if (ioptions.publish_by_id) {
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path_list.add(args.publish_id)
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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}
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32
software/multiqc/main.nf
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32
software/multiqc/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process FASTQC {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: meta.id) }
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conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
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container "quay.io/biocontainers/multiqc:1.9--py_1"
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input:
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tuple val(meta), path("*.html")
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output:
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tuple val(meta), path("multiqc_data"), emit: dir
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tuple val(meta), path("*.html"), emit: html
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${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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"""
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}
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}
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67
software/multiqc/meta.yml
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67
software/multiqc/meta.yml
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name: fastqc
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description: Run FastQC on sequenced reads
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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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tools:
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- fastqc:
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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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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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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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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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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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- 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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- 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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187
software/multiqc/test/input/test_1_fastqc.html
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187
software/multiqc/test/input/test_1_fastqc.html
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BIN
software/multiqc/test/input/test_1_fastqc.zip
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BIN
software/multiqc/test/input/test_1_fastqc.zip
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187
software/multiqc/test/input/test_2_fastqc.html
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187
software/multiqc/test/input/test_2_fastqc.html
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software/multiqc/test/input/test_2_fastqc.zip
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BIN
software/multiqc/test/input/test_2_fastqc.zip
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21
software/multiqc/test/main.nf
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21
software/multiqc/test/main.nf
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#!/usr/bin/env nextflow
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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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/*
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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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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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FASTQC_SE ( input )
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}
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workflow {
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test_single_end()
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}
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6148
software/multiqc/test/multiqc_report.html
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6148
software/multiqc/test/multiqc_report.html
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20
software/multiqc/test/nextflow.config
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20
software/multiqc/test/nextflow.config
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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105
software/multiqc/test/output/multiqc.log
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105
software/multiqc/test/output/multiqc.log
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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
|
||||
3738
software/multiqc/test/output/multiqc_data.json
Normal file
3738
software/multiqc/test/output/multiqc_data.json
Normal file
File diff suppressed because it is too large
Load diff
3
software/multiqc/test/output/multiqc_fastqc.txt
Normal file
3
software/multiqc/test/output/multiqc_fastqc.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
Sample Filename File type Encoding Total Sequences Sequences flagged as poor quality Sequence length %GC total_deduplicated_percentage avg_sequence_length basic_statistics per_base_sequence_quality per_tile_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content
|
||||
test_1 test_1.fastq.gz Conventional base calls Sanger / Illumina 1.9 10000.0 0.0 76.0 44.0 91.72 76.0 pass pass pass pass fail pass pass pass pass warn pass
|
||||
test_2 test_2.fastq.gz Conventional base calls Sanger / Illumina 1.9 10000.0 0.0 76.0 44.0 91.63 76.0 pass pass pass pass fail pass pass pass pass warn pass
|
||||
3
software/multiqc/test/output/multiqc_general_stats.txt
Normal file
3
software/multiqc/test/output/multiqc_general_stats.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
Sample FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences
|
||||
test_1 8.280000000000001 44.0 76.0 9.090909090909092 10000.0
|
||||
test_2 8.370000000000005 44.0 76.0 9.090909090909092 10000.0
|
||||
|
|
@ -0,0 +1 @@
|
|||
Sample
|
||||
3
software/multiqc/test/output/multiqc_sources.txt
Normal file
3
software/multiqc/test/output/multiqc_sources.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
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
|
||||
Loading…
Reference in a new issue