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fix fasta_index_methylseq and fastq_align_dedup workflows #9496

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Merged
sateeshperi merged 4 commits into from
Dec 3, 2025
Merged

fix fasta_index_methylseq and fastq_align_dedup workflows #9496

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feb7b39
fix fasta_index_methylseq and fastq_align_dedup workflows for clarity…
sateeshperi Dec 3, 2025
5015996
fix: pre-commit lint fixes
sateeshperi Dec 3, 2025
9746500
Merge branch 'master' into fix-fasta-index-methylseq
sateeshperi Dec 3, 2025
f768a96
Merge branch 'master' into fix-fasta-index-methylseq
sateeshperi Dec 3, 2025
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72 changes: 40 additions & 32 deletions subworkflows/nf-core/fasta_index_methylseq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
include { UNTAR } from '../../../modules/nf-core/untar/main'
include { UNTAR as UNTAR_BISMARK } from '../../../modules/nf-core/untar/main'
include { UNTAR as UNTAR_BWAMETH } from '../../../modules/nf-core/untar/main'
include { GUNZIP } from '../../../modules/nf-core/gunzip/main'
include { BISMARK_GENOMEPREPARATION as BISMARK_GENOMEPREPARATION_BOWTIE } from '../../../modules/nf-core/bismark/genomepreparation/main'
include { BISMARK_GENOMEPREPARATION as BISMARK_GENOMEPREPARATION_HISAT } from '../../../modules/nf-core/bismark/genomepreparation/main'
Expand All @@ -14,18 +15,18 @@ workflow FASTA_INDEX_METHYLSEQ {
bismark_index // channel: [ val(meta), [ bismark index ] ]
bwameth_index // channel: [ val(meta), [ bwameth index ] ]
bwamem_index // channel: [ val(meta), [ bwamem index ] ]
aligner // string: bismark, bismark_hisat or bwameth
aligner // string: bismark, bismark_hisat, bwameth or bwamem
collecthsmetrics // boolean: whether to run picard collecthsmetrics
use_mem2 // boolean: generate mem2 index if no index provided, and bwameth is selected

main:

ch_fasta = Channel.empty()
ch_fasta_index = Channel.empty()
ch_bismark_index = Channel.empty()
ch_bwameth_index = Channel.empty()
ch_bwamem_index = Channel.empty()
ch_versions = Channel.empty()
ch_fasta = channel.empty()
ch_fasta_index = channel.empty()
ch_bismark_index = channel.empty()
ch_bwameth_index = channel.empty()
ch_bwamem_index = channel.empty()
ch_versions = channel.empty()

// Check if fasta file is gzipped and decompress if needed
fasta
Expand Down Expand Up @@ -56,17 +57,17 @@ workflow FASTA_INDEX_METHYLSEQ {
}
.set { ch_bismark_index_branched }

UNTAR (
UNTAR_BISMARK (
ch_bismark_index_branched.gzipped
)

ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR.out.untar)
ch_versions = ch_versions.mix(UNTAR.out.versions)
ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar)
ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions)
} else {

if( aligner == "bismark_hisat") {
BISMARK_GENOMEPREPARATION_HISAT (
ch_fasta
ch_fasta
)
ch_bismark_index = BISMARK_GENOMEPREPARATION_HISAT.out.index
ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION_HISAT.out.versions)
Expand Down Expand Up @@ -94,39 +95,45 @@ workflow FASTA_INDEX_METHYLSEQ {
}
.set { ch_bwameth_index_branched }

UNTAR (
UNTAR_BWAMETH (
ch_bwameth_index_branched.gzipped
)

ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR.out.untar)
ch_versions = ch_versions.mix(UNTAR.out.versions)
ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR_BWAMETH.out.untar)
ch_versions = ch_versions.mix(UNTAR_BWAMETH.out.versions)
} else {
if (use_mem2) {
BWAMETH_INDEX (
ch_fasta,
true
)
} else {
BWAMETH_INDEX (
ch_fasta,
false
)
}
BWAMETH_INDEX (
ch_fasta,
use_mem2
)
ch_bwameth_index = BWAMETH_INDEX.out.index
ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions)
}
}


else if ( aligner == 'bwamem' ){
log.info "BWA index not provided. Generating BWA index from FASTA file."
/*
* Generate BWA index from FASTA file
*/
if (bwamem_index) {
ch_bwamem_index = bwamem_index
// Handle channel-based bwamem index
bwamem_index
.branch {
gzipped: it[1].toString().endsWith('.gz')
unzipped: true
}
.set { ch_bwamem_index_branched }

UNTAR_BISMARK (
ch_bwamem_index_branched.gzipped
)

ch_bwamem_index = ch_bwamem_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar)
ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions)
} else {
BWA_INDEX(
log.info "BWA index not provided. Generating BWA index from FASTA file."
BWA_INDEX (
ch_fasta
)
ch_bwamem_index = BWA_INDEX.out.index
Expand All @@ -138,11 +145,12 @@ workflow FASTA_INDEX_METHYLSEQ {
* Generate fasta index if not supplied for bwameth workflow or picard collecthsmetrics tool
*/
if (aligner == 'bwameth' || aligner == 'bwamem' || collecthsmetrics) {
// already exising fasta index
// already existing fasta index
if (fasta_index) {
ch_fasta_index = fasta_index
} else {
SAMTOOLS_FAIDX(
log.info "Fasta index not provided. Generating fasta index from FASTA file."
SAMTOOLS_FAIDX (
ch_fasta,
[[:], []],
false
Expand All @@ -157,6 +165,6 @@ workflow FASTA_INDEX_METHYLSEQ {
fasta_index = ch_fasta_index // channel: [ val(meta), [ fasta index ] ]
bismark_index = ch_bismark_index // channel: [ val(meta), [ bismark index ] ]
bwameth_index = ch_bwameth_index // channel: [ val(meta), [ bwameth index ] ]
bwamem_index = ch_bwamem_index // channel: [ val(meta), [ bwamem index ] ]
bwamem_index = ch_bwamem_index // channel: [ val(meta), [ bwamem index ] ]
versions = ch_versions // channel: [ versions.yml ]
}
2 changes: 1 addition & 1 deletion subworkflows/nf-core/fasta_index_methylseq/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ input:
- aligner:
type: string
description: |
Aligner name (bismark, bismark_hisat, or bwameth)
Aligner name (bismark, bismark_hisat, bwameth, or bwamem)
- collecthsmetrics:
type: boolean
description: |
Expand Down
78 changes: 39 additions & 39 deletions subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90,15 +90,15 @@
],
[
"versions.yml:md5,1a7e59286a0e918ba2400750ddefd444",
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:41.408759009"
"timestamp": "2025-12-03T12:20:26.495603"
},
"Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": {
"content": [
Expand Down Expand Up @@ -142,15 +142,15 @@
],
[
"versions.yml:md5,1a7e59286a0e918ba2400750ddefd444",
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:55:10.001932564"
"timestamp": "2025-12-03T12:21:13.279634"
},
"Params: bwameth | generate fasta index | generate bwameth mem2 index": {
"content": [
Expand Down Expand Up @@ -253,15 +253,15 @@

],
[
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97",
"versions.yml:md5,d3ed85f31ec769229e17780530e235ee"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:53:57.304989914"
"timestamp": "2025-12-03T12:19:16.006311"
},
"Params: bwameth | generate fasta index | download bwameth mem2 index | collecthsmetrics": {
"content": [
Expand Down Expand Up @@ -304,15 +304,15 @@
],
[
"versions.yml:md5,1a7e59286a0e918ba2400750ddefd444",
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:55:16.817726661"
"timestamp": "2025-12-03T12:21:24.368005"
},
"Params: bwameth | generate fasta index | download bwameth mem2 index": {
"content": [
Expand Down Expand Up @@ -355,15 +355,15 @@
],
[
"versions.yml:md5,1a7e59286a0e918ba2400750ddefd444",
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:48.244071885"
"timestamp": "2025-12-03T12:20:37.640088"
},
"Params: bwameth | generate fasta index | generate bwameth index": {
"content": [
Expand Down Expand Up @@ -470,15 +470,15 @@

],
[
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97",
"versions.yml:md5,d3ed85f31ec769229e17780530e235ee"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:21.879254265"
"timestamp": "2025-12-03T12:19:53.905574"
},
"Params: bismark_hisat | download bismark index (hisat2)": {
"content": [
Expand Down Expand Up @@ -534,15 +534,15 @@

],
[
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97",
"versions.yml:md5,d3ed85f31ec769229e17780530e235ee"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:15.523551748"
"timestamp": "2025-12-03T12:19:42.978899"
},
"Params: bwameth | download fasta index | download bwameth index": {
"content": [
Expand Down Expand Up @@ -585,15 +585,15 @@

],
[
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:28.152242843"
"timestamp": "2025-12-03T12:20:04.798139"
},
"Params: bwameth | download fasta index | download bwameth mem2 index": {
"content": [
Expand Down Expand Up @@ -635,15 +635,15 @@

],
[
"versions.yml:md5,80527e72159961c33cd9a6d4847e75e3",
"versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69",
"versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-30T10:54:34.434835743"
"timestamp": "2025-12-03T12:20:15.282566"
},
"Params: bwamem | generate fasta index | generate bwamem index": {
"content": [
Expand Down
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