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Add fastq seqkit sana pair (#9185)
* FASTQ_SEQKIT_SANA_PAIR subworkflow init * more tests and meta added * unnecessary operations removed * in one line * Update subworkflows/nf-core/fastq_seqkit_sana_pair/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * meta descr and keywords updated * descr updated * renamed and removed the copying mechanism, replaced with adding/removing strandness on the meta * mandatory config * meta single_end checks --------- Co-authored-by: James A. Fellows Yates <[email protected]>
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‎subworkflows/nf-core/fastq_sanitise_seqkit/main.nf‎

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include { SEQKIT_SANA } from '../../../modules/nf-core/seqkit/sana/main'
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include { SEQKIT_PAIR } from '../../../modules/nf-core/seqkit/pair/main'
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workflow FASTQ_SANITISE_SEQKIT {
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take:
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ch_reads // channel: [ val(meta), [ fastq ] ]
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main:
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ch_versions = Channel.empty()
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// Add strandness information to meta
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ch_reads_with_strandness = ch_reads
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// seqkit/sana can only receive one file at a time
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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 reads should contain two files; a forward and a reverse.")
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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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SEQKIT_SANA( ch_reads_with_strandness )
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ch_versions = ch_versions.mix(SEQKIT_SANA.out.versions.first())
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ch_sanitized_reads = SEQKIT_SANA.out.reads
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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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.branch {
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meta, fastq ->
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single_end: meta.single_end
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return [ meta, fastq ]
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paired_end: !meta.single_end
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return [ meta, fastq ]
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}
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SEQKIT_PAIR ( ch_sanitized_reads.paired_end )
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ch_versions = ch_versions.mix(SEQKIT_PAIR.out.versions.first())
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ch_reads = ch_sanitized_reads.single_end.mix(SEQKIT_PAIR.out.reads, SEQKIT_PAIR.out.unpaired_reads)
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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_sanitise_seqkit/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_sanitise_seqkit"
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description: |
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Filters and reports malformed FASTQ sequences with seqkit/sana,
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and then pairs any paired-end files using seqkit/pair
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keywords:
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- fastq
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- quality control
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- filtering
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- malformed
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- pairing
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- seqkit
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- preprocessing
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components:
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- seqkit/sana
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- seqkit/pair
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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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output:
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- reads:
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type: channel
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description: |
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Channel containing filtered (i.e., non-malformed) and paired FASTQ files.
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For single-end data: returns filtered reads
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For paired-end data: returns properly paired reads and any unpaired reads
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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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- "@vagkaratzas"
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maintainers:
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- "@vagkaratzas"

‎subworkflows/nf-core/fastq_sanitise_seqkit/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_sanitise_seqkit/tests/main.nf.test‎

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nextflow_workflow {
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name "Test Subworkflow FASTQ_SANITISE_SEQKIT"
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script "../main.nf"
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workflow "FASTQ_SANITISE_SEQKIT"
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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 "seqkit"
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tag "seqkit/sana"
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tag "seqkit/pair"
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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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"""
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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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"""
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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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[ 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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}
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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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"""
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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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