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maia-munteanuvagkaratzas
maia-munteanu
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vagkaratzas
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9244 new subworkflow fastq preprocess (#9281)
* remove vscode settings json * restore original vscode json * fix issues --------- Co-authored-by: Evangelos Karatzas <[email protected]>
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‎subworkflows/nf-core/fastq_preprocess/main.nf‎

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include { FASTQ_SANITISE_SEQKIT } from '../fastq_sanitise_seqkit/main'
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include { SEQKIT_SEQ } from '../../../modules/nf-core/seqkit/seq/main'
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include { SEQKIT_REPLACE } from '../../../modules/nf-core/seqkit/replace/main'
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include { SEQKIT_RMDUP } from '../../../modules/nf-core/seqkit/rmdup/main'
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workflow FASTQ_PREPROCESS {
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take:
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ch_reads // channel: [ val(meta), [ fastq ] ]
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skip_seqkit_sana_pair // boolean
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skip_seqkit_seq // boolean
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skip_seqkit_replace // boolean
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skip_seqkit_rmdup // boolean
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main:
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ch_versions = Channel.empty()
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if (!skip_seqkit_sana_pair) {
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FASTQ_SANITISE_SEQKIT( ch_reads )
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ch_reads = FASTQ_SANITISE_SEQKIT.out.reads
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ch_versions = ch_versions.mix(FASTQ_SANITISE_SEQKIT.out.versions.first())
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}
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// Split paired-end reads and add strandedness to meta
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ch_reads_split = ch_reads
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.flatMap { meta, reads ->
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if (meta.single_end) {
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if (reads instanceof List && reads.size() != 1) {
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error("Error: Check your meta.single_end value. Single-end reads should contain one file only.")
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}
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return [[ meta + [strandness: 'single'], reads ]]
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} else {
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if (!(reads instanceof List) || reads.size() != 2) {
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error("Error: Check your meta.single_end value. Paired-end data should have exactly 2 files.")
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}
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return [
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[ meta + [strandness: 'R1'], reads[0] ],
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[ meta + [strandness: 'R2'], reads[1] ]
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]
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}
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}
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if (!skip_seqkit_seq) {
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SEQKIT_SEQ( ch_reads_split )
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ch_reads_split = SEQKIT_SEQ.out.fastx
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ch_versions = ch_versions.mix(SEQKIT_SEQ.out.versions.first())
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}
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if (!skip_seqkit_replace) {
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SEQKIT_REPLACE( ch_reads_split )
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ch_reads_split = SEQKIT_REPLACE.out.fastx
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ch_versions = ch_versions.mix(SEQKIT_REPLACE.out.versions.first())
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}
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if (!skip_seqkit_rmdup) {
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SEQKIT_RMDUP( ch_reads_split )
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ch_reads_split = SEQKIT_RMDUP.out.fastx
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ch_versions = ch_versions.mix(SEQKIT_RMDUP.out.versions.first())
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}
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ch_reads = ch_reads_split
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.map { meta, fastq ->
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// Remove strandness field from meta to merge back together
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def clean_meta = meta.findAll { key, value -> key != 'strandness' }
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return [ clean_meta, fastq ]
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}
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.groupTuple(by: 0)
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.map { meta, files ->
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if (meta.single_end) {
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return [ meta, files[0] ]
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} else {
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def sorted_files = files.flatten().sort { it.name }
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return [ meta, sorted_files ]
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}
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}
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emit:
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reads = ch_reads // channel: [ val(meta), [ fastq ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}

‎subworkflows/nf-core/fastq_preprocess/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
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name: "fastq_preprocess"
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description: Subworkflow that preprocesses FASTQ files
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keywords:
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- fasta
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- seqkit
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- preprocessing
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components:
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- fastq_sanitise_seqkit
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- seqkit/sana
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- seqkit/pair
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- seqkit/seq
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- seqkit/replace
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- seqkit/rmdup
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input:
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- ch_reads:
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type: channel
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description: |
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Channel containing sample metadata and FASTQ files.
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Structure: [ val(meta), [ fastq ] ]
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Where meta is a map containing at least:
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- id: sample identifier
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- single_end: boolean indicating if data is single-end (true) or paired-end (false)
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pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
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- skip_seqkit_sana_pair:
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type: boolean
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description: |
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If true, skips the seqkit_sana_pair subworkflow.
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- skip_seqkit_seq:
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type: boolean
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description: |
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If true, skips the seqkit_seq process.
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- skip_seqkit_replace:
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type: boolean
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description: |
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If true, skips the seqkit_replace process.
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- skip_seqkit_rmdup:
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type: boolean
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description: |
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If true, skips the seqkit_rmdup process.
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output:
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- reads:
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type: channel
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description: |
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Channel containing filtered FASTQ files.
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Structure: [ val(meta), [ fastq ] ]
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pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
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- versions:
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type: file
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description: |
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File containing software versions
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Structure: [ path(versions.yml) ]
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pattern: "versions.yml"
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authors:
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- "@maia-munteanu"
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maintainers:
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- "@maia-munteanu"
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- "@vagkaratzas"

‎subworkflows/nf-core/fastq_preprocess/nextflow.config‎

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// IMPORTANT: This config file should be included to ensure that the subworkflow works properly.
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process {
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withName: SEQKIT_SANA {
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ext.prefix = { "${meta.id}_${meta.strandness}" }
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}
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}

‎subworkflows/nf-core/fastq_preprocess/tests/main.nf.test‎

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nextflow_workflow {
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name "Test Subworkflow FASTQ_PREPROCESS"
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script "../main.nf"
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workflow "FASTQ_PREPROCESS"
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config './nextflow.config'
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tag "subworkflows"
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tag "subworkflows_nfcore"
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tag "subworkflows/fastq_sanitise_seqkit"
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tag "subworkflows/fastq_preprocess"
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tag "seqkit"
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tag "seqkit/sana"
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tag "seqkit/pair"
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tag "seqkit/seq"
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tag "seqkit/replace"
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tag "seqkit/rmdup"
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test("sarscov2 - fastq - single_end") {
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when {
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workflow {
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"""
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input[0] = Channel.of([
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[ id:'test_single', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
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])
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input[1] = false // skip_seqkit_sana_pair
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input[2] = false // skip_seqkit_seq
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input[3] = false // skip_seqkit_replace
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input[4] = false // skip_seqkit_rmdup
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(
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workflow.out,
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workflow.out.versions.collect{ path(it).yaml }.unique()
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).match() }
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)
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}
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}
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test("sarscov2 - fastq - paired_end") {
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when {
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workflow {
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"""
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input[0] = Channel.of([
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[ id:'test_paired', single_end:false ], // meta map
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[
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
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]
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])
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input[1] = false // skip_seqkit_sana_pair
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input[2] = false // skip_seqkit_seq
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input[3] = false // skip_seqkit_replace
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input[4] = false // skip_seqkit_rmdup
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(
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workflow.out,
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workflow.out.versions.collect{ path(it).yaml }.unique()
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).match() }
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)
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}
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}
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test("sarscov2 - fastq - both with single broken") {
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when {
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workflow {
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"""
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input[0] = Channel.of(
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[
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[ id:'test_both', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1_broken.fastq.gz', checkIfExists: true)
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],
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[
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[ id:'test_both', single_end:false ], // meta map
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[
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
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]
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]
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)
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input[1] = false // skip_seqkit_sana_pair
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input[2] = false // skip_seqkit_seq
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input[3] = false // skip_seqkit_replace
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input[4] = false // skip_seqkit_rmdup
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(
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workflow.out,
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workflow.out.versions.collect{ path(it).yaml }.unique()
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).match() }
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)
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}
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}
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test("sarscov2 - fastq - stub") {
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options "-stub"
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when {
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workflow {
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"""
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input[0] = Channel.of([
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[ id: 'test_stub', single_end:true ],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1_broken.fastq.gz', checkIfExists: true)
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])
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input[1] = false // skip_seqkit_sana_pair
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input[2] = false // skip_seqkit_seq
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input[3] = false // skip_seqkit_replace
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input[4] = false // skip_seqkit_rmdup
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(
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workflow.out,
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workflow.out.versions.collect{ path(it).yaml }.unique()
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).match() }
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)
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}
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}
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}

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