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Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests #9519

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124 changes: 124 additions & 0 deletions subworkflows/nf-core/fastq_remove_adapters_and_merge/main.nf
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// ok for single end adapter removal
include { TRIMMOMATIC } from '../../../modules/nf-core/trimmomatic/main'
include { CUTADAPT } from '../../../modules/nf-core/cutadapt/main'
include { TRIMGALORE } from '../../../modules/nf-core/trimgalore/main'
include { BBMAP_BBDUK } from '../../../modules/nf-core/bbmap/bbduk/main'

// allows merging of paired end reads, but will work for single end reads as well
include { FASTP } from '../../../modules/nf-core/fastp/main'
include { ADAPTERREMOVAL} from '../../../modules/nf-core/adapterremoval/main'
include { LEEHOM } from '../../../modules/nf-core/leehom/main'

// requirs paired end becouse of merging
include { NGMERGE } from '../../../modules/nf-core/ngmerge/main'

workflow FASTQ_REMOVE_ADAPTERS_AND_MERGE {

take:
reads // (meta, reads) - SE or PE
skip_trimmomatic // boolean
skip_cutadapt
skip_trimgalore
skip_bbduk
skip_fastp
skip_adapterremoval
skip_leehom
skip_ngmerge
do_merge
adapters_contaminants
main:

ch_current = reads
ch_versions = Channel.empty()

if (!skip_trimmomatic) {
// TRIMMOMATIC.ext.adapters = adapters_contaminants
TRIMMOMATIC( ch_current )
ch_current = TRIMMOMATIC.out.trimmed_reads.map { meta, r -> [meta, r] }
ch_versions = ch_versions.mix(TRIMMOMATIC.out.versions)
}

if (!skip_cutadapt) {
CUTADAPT( ch_current )
ch_current = CUTADAPT.out.reads.map { meta, r -> [meta, r] }
ch_versions = ch_versions.mix(CUTADAPT.out.versions)
}

if (!skip_trimgalore) {
TRIMGALORE( ch_current )
ch_current = TRIMGALORE.out.reads.map { meta, r -> [meta, r] }
ch_versions = ch_versions.mix(TRIMGALORE.out.versions)
}

if (!skip_bbduk) {
ch_current.view { "DEBUG: BEFORE BBMAP_BBDUK → $it" }
BBMAP_BBDUK( ch_current, adapters_contaminants )
ch_current = BBMAP_BBDUK.out.reads.map { meta, r -> [meta, r] }
ch_versions = ch_versions.mix(BBMAP_BBDUK.out.versions)
ch_current.view { "DEBUG: AFTER BBMAP_BBDUK → $it" }
}

if (!skip_fastp && !do_merge) {
ch_current.view { "DEBUG: BEFORE FASTP → $it" }
FASTP( ch_current.map { meta, r -> tuple(meta, r, adapters_contaminants)},
false,
true,
do_merge)
ch_current = FASTP.out.reads.map { meta, r -> [meta, r] }
ch_versions = ch_versions.mix(FASTP.out.versions)
ch_current.view { "DEBUG: AFTER FASTP → $it" }
}

if (!skip_adapterremoval && !do_merge) {
ADAPTERREMOVAL( ch_current, adapters_contaminants )
ch_current.view { "DEBUG: BEFORE ADAPTERREMOVAL → $it" }
ch_current = ADAPTERREMOVAL.out.paired_truncated
.mix(ADAPTERREMOVAL.out.singles_truncated)
.map { tup ->
def meta = tup[0]
def r = tup[1]
[meta, r]
}
ch_versions = ch_versions.mix(ADAPTERREMOVAL.out.versions)
ch_current.view { "DEBUG: AFTER ADAPTERREMOVAL → $it" }
}

if (!skip_leehom && !do_merge) {
ch_current.view { "DEBUG: BEFORE LEEHOM → $it" }
ch_leehom_input = ch_current.map { meta, r ->
if (meta.single_end)
return [meta, r]
else
return [meta, [reads[0], reads[1]]]
}

LEEHOM(ch_leehom_input)

ch_leehom_pe =
LEEHOM.out.unmerged_r1_fq_pass
.combine(LEEHOM.out.unmerged_r2_fq_pass)
.map { left, right ->
def meta = left[0]
def r1 = left[1]
def r2 = right[1]
[meta, [r1, r2]]
}
.filter { meta, r -> !meta.single_end } // only PE

// ---- SE OUTPUT ----
ch_leehom_se =
LEEHOM.out.fq_pass
.filter { meta, r -> meta.single_end }
.map { meta, r -> [meta, r] }

// ---- MERGE CHANNELS ----
ch_current = ch_leehom_pe.mix(ch_leehom_se)

ch_versions = ch_versions.mix(LEEHOM.out.versions)
}

emit:

trimmed_reads = ch_current // channel: [ meta, trimmed_reads ]
versions = ch_versions // channel: [ versions.yml ]
}
51 changes: 51 additions & 0 deletions subworkflows/nf-core/fastq_remove_adapters_and_merge/meta.yml
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "fastq_remove_adapters_and_merge"
## TODO nf-core: Add a description of the subworkflow and list keywords
description: Sort SAM/BAM/CRAM file
keywords:
- sort
- bam
- sam
- cram
## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
components:
- samtools/sort
- samtools/index
## TODO nf-core: List all of the channels used as input with a description and their structure
input:
- ch_bam:
type: file
description: |
The input channel containing the BAM/CRAM/SAM files
Structure: [ val(meta), path(bam) ]
pattern: "*.{bam/cram/sam}"
## TODO nf-core: List all of the channels used as output with a descriptions and their structure
output:
- bam:
type: file
description: |
Channel containing BAM files
Structure: [ val(meta), path(bam) ]
pattern: "*.bam"
- bai:
type: file
description: |
Channel containing indexed BAM (BAI) files
Structure: [ val(meta), path(bai) ]
pattern: "*.bai"
- csi:
type: file
description: |
Channel containing CSI files
Structure: [ val(meta), path(csi) ]
pattern: "*.csi"
- versions:
type: file
description: |
File containing software versions
Structure: [ path(versions.yml) ]
pattern: "versions.yml"
authors:
- "@kornkv"
maintainers:
- "@kornkv"
95 changes: 95 additions & 0 deletions subworkflows/nf-core/fastq_remove_adapters_and_merge/tests/main.nf.test
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nextflow_workflow {

name "Test Subworkflow FASTQ_REMOVE_ADAPTERS_AND_MERGE"
script "../main.nf"
workflow "FASTQ_REMOVE_ADAPTERS_AND_MERGE"

tag "subworkflows"
tag "trimmomatic"
tag "cutadapt"
tag "trimgalore"
tag "bbmap/bbduk"
tag "fastp"
tag "adapterremoval"
tag "leehom"
tag "ngmerge"

/**************************************************************
* TEST 1 — SINGLE END
**************************************************************/
test("sarscov2 - fastq - single-end") {
config "./nextflow.config"
when {
workflow {
"""
input[0] = [
[ id:'test', single_end:true ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]

input[1] = false // skip_trimmomatic
input[2] = false // skip_cutadapt
input[3] = false // skip_trimgalore
input[4] = false // skip_bbduk
input[5] = false // skip_fastp
input[6] = false // skip_adapterremoval
input[7] = false // skip_leehom
input[8] = true // skip_ngmerge
input[9] = false // do_merge
input[10] = []
"""
}
}

then {
assert workflow.success

assert snapshot(
workflow.out.trimmed_reads.sort(),
workflow.out.versions.collect { path(it).yaml }.sort()
).match()
}
}


/**************************************************************
* TEST 2 — PAIRED END
**************************************************************/
test("sarscov2 - fastq - paired-end, no merging") {
config "./nextflow.config"
when { params {
samtools_arg = ''
}
workflow {
"""
input[0] = [
[ id:'test_paired', single_end:false ],
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]

input[1] = false // skip_trimmomatic
input[2] = false // skip_cutadapt
input[3] = false // skip_trimgalore
input[4] = false // skip_bbduk
input[5] = false // skip_fastp
input[6] = false // skip_adapterremoval
input[7] = false // skip_leehom
input[8] = true // skip_ngmerge
input[9] = false // do_merge
input[10] = []
"""
}
}

then {
assertAll(
{ assert workflow.success },
{ assert snapshot(workflow.out).match() }
)
}
}

}
92 changes: 92 additions & 0 deletions subworkflows/nf-core/fastq_remove_adapters_and_merge/tests/main.nf.test.snap
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{
"sarscov2 - fastq - paired-end, no merging": {
"content": [
{
"0": [

],
"1": [
"versions.yml:md5,2d964cf60309a142f1c9958da875eb54",
"versions.yml:md5,90401b38cbb7e43510ca1a7cbcea3145",
"versions.yml:md5,95732be10dd312717626b93c727886ef",
"versions.yml:md5,aa5ed9a565951378f5d671bfa6b88370",
"versions.yml:md5,b9c8e5d6936d4d2dbc08084d03ee57c8",
"versions.yml:md5,de9c9c39a848b9543456f693e4ca6ad3"
],
"trimmed_reads": [

],
"versions": [
"versions.yml:md5,2d964cf60309a142f1c9958da875eb54",
"versions.yml:md5,90401b38cbb7e43510ca1a7cbcea3145",
"versions.yml:md5,95732be10dd312717626b93c727886ef",
"versions.yml:md5,aa5ed9a565951378f5d671bfa6b88370",
"versions.yml:md5,b9c8e5d6936d4d2dbc08084d03ee57c8",
"versions.yml:md5,de9c9c39a848b9543456f693e4ca6ad3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-12-08T10:34:07.314632994"
},
"sarscov2 - fastq - single-end": {
"content": [
[
[
{
"id": "test",
"single_end": true
},
"test.fq.gz:md5,6dcea64429b2bcf5e31751f9c8041914"
]
],
[
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:FASTP": {
"fastp": "1.0.1"
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:LEEHOM": {
"leehom": "1.2.15"
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:ADAPTERREMOVAL": {
"adapterremoval": "2.3.2"
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:TRIMMOMATIC": {
"trimmomatic": 0.39
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:BBMAP_BBDUK": {
"bbmap": 39.18
}
},
{
"FASTQ_REMOVE_ADAPTERS_AND_MERGE:CUTADAPT": {
"cutadapt": 5.0
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-12-08T10:33:53.838298621"
}
}
17 changes: 17 additions & 0 deletions subworkflows/nf-core/fastq_remove_adapters_and_merge/tests/nextflow.config
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process {

withName: TRIMMOMATIC {
ext.args = {
def adapters = "TruSeq3-SE.fa"
"ILLUMINACLIP:${adapters}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
}
}

withName: CUTADAPT {
ext.args = '-q 25'
}
withName: BBMAP_BBDUK {
ext.args = 'trimq=10 qtrim=r'
ext.prefix = { "${meta.id}.trim" }
}
}
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