mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 20:43:09 +00:00
Get skeleton read processing to input for profiling
This commit is contained in:
parent
1b893cb039
commit
cf55cc592c
13 changed files with 407 additions and 27 deletions
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@ -42,9 +42,9 @@ On release, automated continuous integration tests run the pipeline on a full-si
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- Centrifuge
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- Kaiju
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- mOTUs
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4. Perform optional post-processing with:
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- bracken
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5. Standardises output tables
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4. Perform optional post-processing with:
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- bracken
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5. Standardises output tables
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6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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## Quick Start
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@ -28,8 +28,47 @@ process {
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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path: { "${params.outdir}/fastqc/raw" },
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mode: 'copy',
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pattern: '*.html'
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]
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}
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withName: FASTP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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// TODO also include option to NOT merge
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ext.args = [
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{ ${meta.single_end} } == 0 ? "-m" : '',
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params.fastp_exclude_unmerged ? '' : "--include_unmerged"
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].join(' ').trim()
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: FASTQC_POST {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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pattern: '*.html'
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]
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}
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withName: CAT_FASTQ {
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publishDir = [
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path: { "${params.outdir}/prepared_sequences" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -22,8 +22,6 @@ params {
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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// Genome references
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genome = 'R64-1-1'
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}
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@ -10,10 +10,11 @@ class WorkflowTaxprofiler {
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public static void initialise(params, log) {
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genomeExistsError(params, log)
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if (!params.fasta) {
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log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
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System.exit(1)
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}
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// TODO update as necessary
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//if (!params.fasta) {
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// log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
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// System.exit(1)
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//}
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}
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//
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@ -3,9 +3,15 @@
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"homePage": "https://github.com/nf-core/taxprofiler",
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"repos": {
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"nf-core/modules": {
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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"custom/dumpsoftwareversions": {
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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},
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"fastp": {
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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},
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"fastqc": {
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"git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
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},
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51
modules/nf-core/modules/cat/fastq/main.nf
generated
Normal file
51
modules/nf-core/modules/cat/fastq/main.nf
generated
Normal file
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@ -0,0 +1,51 @@
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process CAT_FASTQ {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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'biocontainers/biocontainers:v1.2.0_cv1' }"
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input:
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tuple val(meta), path(reads, stageAs: "input*/*")
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output:
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tuple val(meta), path("*.merged.fastq.gz"), emit: reads
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def readList = reads.collect{ it.toString() }
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if (meta.single_end) {
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if (readList.size > 1) {
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"""
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cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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} else {
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if (readList.size > 2) {
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def read1 = []
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def read2 = []
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readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
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"""
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cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
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cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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}
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}
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39
modules/nf-core/modules/cat/fastq/meta.yml
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39
modules/nf-core/modules/cat/fastq/meta.yml
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Normal file
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name: cat_fastq
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description: Concatenates fastq files
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keywords:
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- fastq
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- concatenate
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tools:
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- cat:
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description: |
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The cat utility reads files sequentially, writing them to the standard output.
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documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
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licence: ["GPL-3.0-or-later"]
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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: list
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description: |
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List of input FastQ files to be concatenated.
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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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- reads:
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type: file
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description: Merged fastq file
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pattern: "*.{merged.fastq.gz}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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75
modules/nf-core/modules/fastp/main.nf
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75
modules/nf-core/modules/fastp/main.nf
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Normal file
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process FASTP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
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'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
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input:
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tuple val(meta), path(reads)
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val save_trimmed_fail
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val save_merged
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output:
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tuple val(meta), path('*.trim.fastq.gz') , optional:true, emit: reads
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tuple val(meta), path('*.json') , emit: json
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tuple val(meta), path('*.html') , emit: html
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail
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tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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// Added soft-links to original fastqs for consistent naming in MultiQC
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
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fastp \\
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--in1 ${prefix}.fastq.gz \\
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--out1 ${prefix}.trim.fastq.gz \\
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--thread $task.cpus \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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$fail_fastq \\
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$args \\
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2> ${prefix}.fastp.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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END_VERSIONS
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"""
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} else {
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def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
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def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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fastp \\
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--in1 ${prefix}_1.fastq.gz \\
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--in2 ${prefix}_2.fastq.gz \\
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--out1 ${prefix}_1.trim.fastq.gz \\
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--out2 ${prefix}_2.trim.fastq.gz \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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$fail_fastq \\
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$merge_fastq \\
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--thread $task.cpus \\
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--detect_adapter_for_pe \\
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$args \\
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2> ${prefix}.fastp.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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END_VERSIONS
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"""
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}
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}
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68
modules/nf-core/modules/fastp/meta.yml
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Normal file
68
modules/nf-core/modules/fastp/meta.yml
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Normal file
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name: fastp
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description: Perform adapter/quality trimming on sequencing reads
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keywords:
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- trimming
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- quality control
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- fastq
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tools:
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- fastp:
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description: |
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A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
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documentation: https://github.com/OpenGene/fastp
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doi: https://doi.org/10.1093/bioinformatics/bty560
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licence: ["MIT"]
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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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- save_trimmed_fail:
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type: boolean
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description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
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- save_merged:
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type: boolean
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description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
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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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- reads:
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type: file
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description: The trimmed/modified/unmerged fastq reads
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pattern: "*trim.fastq.gz"
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- json:
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type: file
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description: Results in JSON format
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pattern: "*.json"
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- html:
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type: file
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description: Results in HTML format
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pattern: "*.html"
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- log:
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type: file
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description: fastq log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- reads_fail:
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type: file
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description: Reads the failed the preprocessing
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pattern: "*fail.fastq.gz"
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- reads_merged:
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type: file
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description: Reads that were successfully merged
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pattern: "*.{merged.fastq.gz}"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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@ -33,7 +33,7 @@ params {
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help = false
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validate_params = true
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show_hidden_params = false
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schema_ignore_params = 'genomes'
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schema_ignore_params = 'genomes,fasta'
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enable_conda = false
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// Config options
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max_cpus = 16
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max_time = '240.h'
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// FASTQ preprocessing
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fastp_clip_merge = false
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fastp_exclude_unmerged = true
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}
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// Load base.config by default for all pipelines
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@ -56,15 +56,6 @@
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"fa_icon": "fas fa-book",
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"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
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},
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"fasta": {
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"type": "string",
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"format": "file-path",
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
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"description": "Path to FASTA genome file.",
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"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
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"fa_icon": "far fa-file-code"
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},
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"igenomes_base": {
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"type": "string",
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"format": "directory-path",
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@ -9,22 +9,38 @@ workflow INPUT_CHECK {
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samplesheet // file: /path/to/samplesheet.csv
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main:
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SAMPLESHEET_CHECK ( samplesheet )
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parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
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.csv
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.splitCsv ( header:true, sep:',' )
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.dump(tag: "split_csv_out")
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.branch {
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fasta: it['fasta'] != ''
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fastq: true
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}
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parsed_samplesheet.fastq
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.map { create_fastq_channels(it) }
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.set { reads }
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.dump(tag: "fastq_channel_init")
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.set { fastq }
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parsed_samplesheet.fasta
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.map { create_fasta_channels(it) }
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.dump(tag: "fasta_channel_init")
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.set { fasta }
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emit:
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reads // channel: [ val(meta), [ reads ] ]
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fastq // channel: [ val(meta), [ reads ] ]
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fasta // channel: [ val(meta), fasta ]
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versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
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}
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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def create_fastq_channels(LinkedHashMap row) {
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def meta = [:]
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meta.id = row.sample
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meta.single_end = row.single_end.toBoolean()
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meta.id = row.sample
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = row.single_end.toBoolean()
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def array = []
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if (!file(row.fastq_1).exists()) {
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@ -40,3 +56,20 @@ def create_fastq_channels(LinkedHashMap row) {
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}
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return array
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}
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// Function to get list of [ meta, fasta ]
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def create_fasta_channels(LinkedHashMap row) {
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def meta = [:]
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meta.id = row.sample
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = true
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||||
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def array = []
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if (!file(row.fasta).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}"
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}
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array = [ meta, [ file(row.fasta) ] ]
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||||
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||||
return array
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||||
}
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@ -11,7 +11,7 @@ WorkflowTaxprofiler.initialise(params, log)
|
|||
|
||||
// TODO nf-core: Add all file path parameters for the pipeline to the list below
|
||||
// Check input path parameters to see if they exist
|
||||
def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
|
||||
def checkPathParamList = [ params.input, params.multiqc_config ]
|
||||
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
||||
|
||||
// Check mandatory parameters
|
||||
|
@ -50,6 +50,11 @@ include { FASTQC } from '../modules/nf-core/modules/fastqc/
|
|||
include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
|
||||
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
|
||||
|
||||
include { FASTP as FASTP_SINGLE } from '../modules/nf-core/modules/fastp/main'
|
||||
include { FASTP as FASTP_PAIRED } from '../modules/nf-core/modules/fastp/main'
|
||||
include { FASTQC as FASTQC_POST } from '../modules/nf-core/modules/fastqc/main'
|
||||
include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
|
||||
|
||||
/*
|
||||
========================================================================================
|
||||
RUN MAIN WORKFLOW
|
||||
|
@ -75,7 +80,7 @@ workflow TAXPROFILER {
|
|||
// MODULE: Run FastQC
|
||||
//
|
||||
FASTQC (
|
||||
INPUT_CHECK.out.reads
|
||||
INPUT_CHECK.out.fastq
|
||||
)
|
||||
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
|
||||
|
||||
|
@ -83,6 +88,71 @@ workflow TAXPROFILER {
|
|||
ch_versions.unique().collectFile(name: 'collated_versions.yml')
|
||||
)
|
||||
|
||||
//
|
||||
// MODULE: Run Clip/Merge/Complexity
|
||||
//
|
||||
// TODO give option to clip only and retain pairs
|
||||
// TODO give option to retain singletons (probably fastp option likely)
|
||||
// TODO move to subworkflow
|
||||
if ( params.fastp_clip_merge ) {
|
||||
|
||||
ch_input_for_fastp = INPUT_CHECK.out.fastq
|
||||
.dump(tag: "pre-fastp_branch")
|
||||
.branch{
|
||||
single: it[0]['single_end'] == true
|
||||
paired: it[0]['single_end'] == false
|
||||
}
|
||||
|
||||
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
|
||||
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
|
||||
|
||||
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
|
||||
FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
|
||||
|
||||
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
|
||||
.mix( FASTP_SINGLE.out.reads )
|
||||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
meta_new['single_end'] = 1
|
||||
[ meta_new, reads ]
|
||||
}
|
||||
|
||||
FASTQC_POST ( ch_fastp_reads_prepped )
|
||||
|
||||
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
|
||||
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
|
||||
|
||||
ch_processed_reads = ch_fastp_reads_prepped
|
||||
|
||||
} else {
|
||||
ch_processed_reads = INPUT_CHECK.out.fastq
|
||||
}
|
||||
|
||||
|
||||
// MODULE: Cat merge runs of same sample
|
||||
ch_processed_for_combine = ch_processed_reads
|
||||
.dump(tag: "prep_for_combine_grouping")
|
||||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
meta_new['run_accession'] = 'combined'
|
||||
[ meta_new, reads ]
|
||||
}
|
||||
.groupTuple ( by: 0 )
|
||||
.branch{
|
||||
combine: it[1].size() >= 2
|
||||
skip: it[1].size() < 2
|
||||
}
|
||||
|
||||
CAT_FASTQ ( ch_processed_for_combine.combine )
|
||||
|
||||
// Ready for profiling!
|
||||
ch_reads_for_profiling = ch_processed_for_combine.skip
|
||||
.dump(tag: "skip_combine")
|
||||
.mix( CAT_FASTQ.out.reads )
|
||||
.dump(tag: "files_for_profiling")
|
||||
|
||||
//
|
||||
// MODULE: MultiQC
|
||||
//
|
||||
|
@ -95,6 +165,12 @@ workflow TAXPROFILER {
|
|||
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
||||
if (params.fastp_clip_merge) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTP_SINGLE.out.json.collect{it[1]}.ifEmpty([]))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTP_PAIRED.out.json.collect{it[1]}.ifEmpty([]))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC_POST.out.zip.collect{it[1]}.ifEmpty([]))
|
||||
}
|
||||
|
||||
|
||||
MULTIQC (
|
||||
ch_multiqc_files.collect()
|
||||
|
|
Loading…
Reference in a new issue