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rename to more appropriate fastq_preprocess_seqkit #9537

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Merged
vagkaratzas merged 1 commit into from
Dec 9, 2025
Merged

rename to more appropriate fastq_preprocess_seqkit #9537

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23 changes: 11 additions & 12 deletions ...orkflows/nf-core/fastq_preprocess/main.nf → ...s/nf-core/fastq_preprocess_seqkit/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,22 +3,22 @@ include { SEQKIT_SEQ } from '../../../modules/nf-core/seqkit/seq/main
include { SEQKIT_REPLACE } from '../../../modules/nf-core/seqkit/replace/main'
include { SEQKIT_RMDUP } from '../../../modules/nf-core/seqkit/rmdup/main'

workflow FASTQ_PREPROCESS {
workflow FASTQ_PREPROCESS_SEQKIT {

take:
ch_reads // channel: [ val(meta), [ fastq ] ]
skip_seqkit_sana_pair // boolean
skip_seqkit_seq // boolean
skip_seqkit_replace // boolean
skip_seqkit_rmdup // boolean
ch_reads // channel: [ val(meta), [ fastq ] ]
skip_seqkit_sana_pair // boolean
skip_seqkit_seq // boolean
skip_seqkit_replace // boolean
skip_seqkit_rmdup // boolean

main:
ch_versions = Channel.empty()
ch_versions = channel.empty()

if (!skip_seqkit_sana_pair) {
FASTQ_SANITISE_SEQKIT( ch_reads )
ch_reads = FASTQ_SANITISE_SEQKIT.out.reads
ch_versions = ch_versions.mix(FASTQ_SANITISE_SEQKIT.out.versions.first())
ch_reads = FASTQ_SANITISE_SEQKIT.out.reads
ch_versions = ch_versions.mix(FASTQ_SANITISE_SEQKIT.out.versions)
}

// Split paired-end reads and add strandedness to meta
Expand Down Expand Up @@ -75,7 +75,6 @@ workflow FASTQ_PREPROCESS {
}

emit:
reads = ch_reads // channel: [ val(meta), [ fastq ] ]
versions = ch_versions // channel: [ versions.yml ]

reads = ch_reads // channel: [ val(meta), [ fastq ] ]
versions = ch_versions // channel: [ versions.yml ]
}
4 changes: 2 additions & 2 deletions ...rkflows/nf-core/fastq_preprocess/meta.yml → .../nf-core/fastq_preprocess_seqkit/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "fastq_preprocess"
name: "fastq_preprocess_seqkit"
description: Subworkflow that preprocesses FASTQ files
keywords:
- fasta
- fastq
- seqkit
- preprocessing
components:
Expand Down
2 changes: 0 additions & 2 deletions .../nf-core/fastq_preprocess/nextflow.config → ...e/fastq_preprocess_seqkit/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
// IMPORTANT: This config file should be included to ensure that the subworkflow works properly.
process {

withName: SEQKIT_SANA {
ext.prefix = { "${meta.id}_${meta.strandness}" }
}

}
6 changes: 3 additions & 3 deletions ...-core/fastq_preprocess/tests/main.nf.test → ...astq_preprocess_seqkit/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
nextflow_workflow {

name "Test Subworkflow FASTQ_PREPROCESS"
name "Test Subworkflow FASTQ_PREPROCESS_SEQKIT"
script "../main.nf"
workflow "FASTQ_PREPROCESS"
workflow "FASTQ_PREPROCESS_SEQKIT"
config './nextflow.config'

tag "subworkflows"
tag "subworkflows_nfcore"
tag "subworkflows/fastq_sanitise_seqkit"
tag "subworkflows/fastq_preprocess"
tag "subworkflows/fastq_preprocess_seqkit"
tag "seqkit"
tag "seqkit/sana"
tag "seqkit/pair"
Expand Down
138 changes: 76 additions & 62 deletions .../fastq_preprocess/tests/main.nf.test.snap → ...preprocess_seqkit/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@
]
],
"1": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
],
"reads": [
[
Expand All @@ -27,40 +27,40 @@
]
],
"versions": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
]
},
[
{
"FASTQ_PREPROCESS:SEQKIT_REPLACE": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
}
},
{
"FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": {
"seqkit": "v2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_RMDUP": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-29T13:17:10.915765"
"timestamp": "2025-12-09T16:30:14.034664087"
},
"sarscov2 - fastq - single_end": {
"content": [
Expand All @@ -75,10 +75,10 @@
]
],
"1": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
],
"reads": [
[
Expand All @@ -90,40 +90,40 @@
]
],
"versions": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
]
},
[
{
"FASTQ_PREPROCESS:SEQKIT_REPLACE": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
}
},
{
"FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": {
"seqkit": "v2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_RMDUP": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-29T13:16:51.34468"
"timestamp": "2025-12-09T16:29:39.447454093"
},
"sarscov2 - fastq - paired_end": {
"content": [
Expand All @@ -141,10 +141,11 @@
]
],
"1": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6",
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
],
"reads": [
[
Expand All @@ -159,40 +160,46 @@
]
],
"versions": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6",
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
]
},
[
{
"FASTQ_PREPROCESS:SEQKIT_REPLACE": {
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_PAIR": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_RMDUP": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": {
"seqkit": "v2.9.0"
}
},
{
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-29T13:16:58.073323"
"timestamp": "2025-12-09T16:29:51.089592083"
},
"sarscov2 - fastq - both with single broken": {
"content": [
Expand All @@ -217,10 +224,11 @@
]
],
"1": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6",
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
],
"reads": [
[
Expand All @@ -242,39 +250,45 @@
]
],
"versions": [
"versions.yml:md5,12eff6cdaef31b58e36df720f8d96331",
"versions.yml:md5,8352db48172cddc55e42f943cdee1b9a",
"versions.yml:md5,9afc673105901c4307e8bb20d367a3ce",
"versions.yml:md5,d4403f4032d4cbb377d61ed83712253e"
"versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6",
"versions.yml:md5,39b373e11c89d8445dd09c9ae185e543",
"versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd",
"versions.yml:md5,edb80840a6bf15376776a917a0f36216",
"versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6"
]
},
[
{
"FASTQ_PREPROCESS:SEQKIT_REPLACE": {
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_PAIR": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": {
"seqkit": "2.9.0"
}
},
{
"FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": {
"seqkit": "2.10.1"
}
},
{
"FASTQ_PREPROCESS:SEQKIT_RMDUP": {
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": {
"seqkit": "v2.9.0"
}
},
{
"FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": {
"seqkit": "v2.9.0"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-29T13:17:05.485679"
"timestamp": "2025-12-09T16:30:03.379196661"
}
}
2 changes: 0 additions & 2 deletions ...re/fastq_preprocess/tests/nextflow.config → ...q_preprocess_seqkit/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
process {

withName: SEQKIT_SANA {
ext.prefix = { "${meta.id}_${meta.strandness}" }
}
Expand All @@ -24,5 +23,4 @@ process {
withName: SEQKIT_RMDUP {
ext.prefix = { "${meta.id}_${meta.strandness}" }
}

}
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