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Added stub logic and test to fastq_fastqc_umitools_fastp (#5858)
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* Added stub logic and test to fastq_fastqc_umitools_fastp

* Now emitting trimmed reads
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@GallVp
GallVp authored Jun 21, 2024
1 parent 2aee476 commit db35d26
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Showing 3 changed files with 278 additions and 2 deletions.
10 changes: 8 additions & 2 deletions subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,18 @@ include { FASTP } from '../../../modules/nf-core/fastp/main'
//
import groovy.json.JsonSlurper

def getFastpReadsAfterFiltering(json_file) {
def getFastpReadsAfterFiltering(json_file, min_num_reads) {

if ( workflow.stubRun ) { return min_num_reads }

def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
return json['after_filtering']['total_reads'].toLong()
}

def getFastpAdapterSequence(json_file){

if ( workflow.stubRun ) { return "" }

def Map json = (Map) new JsonSlurper().parseText(json_file.text)
try{
adapter = json['adapter_cutting']['read1_adapter_sequence']
Expand Down Expand Up @@ -109,7 +115,7 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
.out
.reads
.join(trim_json)
.map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json) ] }
.map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json, min_trimmed_reads.toLong()) ] }
.set { ch_num_trimmed_reads }

ch_num_trimmed_reads
Expand Down
45 changes: 45 additions & 0 deletions subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -559,4 +559,49 @@ nextflow_workflow {
)
}
}

test("sarscov2 paired-end [fastq] - stub") {

options '-stub'

when {
workflow {
"""
skip_fastqc = false
with_umi = false
skip_umi_extract = false
umi_discard_read = 1
skip_trimming = false
adapter_fasta = []
save_trimmed_fail = false
save_merged = false
min_trimmed_reads = 1
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
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] = skip_fastqc
input[2] = with_umi
input[3] = skip_umi_extract
input[4] = umi_discard_read
input[5] = skip_trimming
input[6] = adapter_fasta
input[7] = save_trimmed_fail
input[8] = save_merged
input[9] = min_trimmed_reads
"""
}
}

then {
assertAll(
{ assert workflow.success },
{ assert snapshot(workflow.out).match() }
)
}
}
}
225 changes: 225 additions & 0 deletions subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -545,5 +545,230 @@
"nextflow": "24.04.2"
},
"timestamp": "2024-06-10T15:08:32.267769943"
},
"sarscov2 paired-end [fastq] - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"10": [
[
{
"id": "test",
"single_end": false
},
1
]
],
"11": [
[
{
"id": "test",
"single_end": false
},
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"12": [
[
{
"id": "test",
"single_end": false
},
"test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"13": [
"versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
"versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
"versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [

],
"4": [
[
{
"id": "test",
"single_end": false
},
""
]
],
"5": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"6": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"7": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"8": [

],
"9": [

],
"adapter_seq": [
[
{
"id": "test",
"single_end": false
},
""
]
],
"fastqc_raw_html": [
[
{
"id": "test",
"single_end": false
},
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"fastqc_raw_zip": [
[
{
"id": "test",
"single_end": false
},
"test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"fastqc_trim_html": [
[
{
"id": "test",
"single_end": false
},
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"fastqc_trim_zip": [
[
{
"id": "test",
"single_end": false
},
"test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"reads": [
[
{
"id": "test",
"single_end": false
},
[
"test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"trim_html": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"trim_json": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"trim_log": [
[
{
"id": "test",
"single_end": false
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"trim_read_count": [
[
{
"id": "test",
"single_end": false
},
1
]
],
"trim_reads_fail": [

],
"trim_reads_merged": [

],
"umi_log": [

],
"versions": [
"versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
"versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
"versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T14:46:58.329605"
}
}

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