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Merged
LouisLeNezet merged 22 commits into from
Mar 2, 2026
Merged

Add new sbwf BAM_VARIANT_CALLING_MPILEUP_BCFTOOLS #10283

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2678803
Create sbwf
LouisLeNezet Feb 3, 2026
343dbc8
Fix sbwf
Feb 27, 2026
2fababf
Merge branch 'master' into bam_gl_bcftools
LouisLeNezet Feb 27, 2026
41748d9
Update merge
Feb 27, 2026
9c0f9fe
Update merge
Feb 27, 2026
b684b63
Update bcftools annotate
Feb 27, 2026
7900e47
Update sbwf
Feb 27, 2026
8341777
Merge branch 'master' into bam_gl_bcftools
LouisLeNezet Feb 27, 2026
648ff71
Fix test
Feb 27, 2026
61421a7
Update mpileup
Feb 27, 2026
32cd6d0
Update tests
Feb 27, 2026
ac93c7c
Sort metas
Feb 27, 2026
888532e
Update subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/meta…
LouisLeNezet Feb 27, 2026
05eed4e
Update tags
Feb 27, 2026
575fba8
Update snapshot
Feb 27, 2026
63e908e
Update intervals
LouisLeNezet Mar 2, 2026
07ebf16
Fix comments
LouisLeNezet Mar 2, 2026
bba5258
Update subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/main.nf
LouisLeNezet Mar 2, 2026
4947a4f
Update subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/main.nf
LouisLeNezet Mar 2, 2026
a54c7f7
Update subworkflows/nf-core/bam_variant_calling_mpileup_bcftools/main.nf
LouisLeNezet Mar 2, 2026
c5d1a61
Merge branch 'master' into bam_gl_bcftools
LouisLeNezet Mar 2, 2026
58d82c0
Fix sbwf
LouisLeNezet Mar 2, 2026
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5 changes: 1 addition & 4 deletions modules/nf-core/bcftools/annotate/main.nf
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Expand Up @@ -8,10 +8,7 @@ process BCFTOOLS_ANNOTATE {
: 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}"

input:
tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
path columns
path header_lines
path rename_chrs
tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(columns), path(header_lines), path(rename_chrs)

output:
tuple val(meta), path("${prefix}.${extension}"), emit: vcf
Expand Down
26 changes: 13 additions & 13 deletions modules/nf-core/bcftools/annotate/meta.yml
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Expand Up @@ -36,19 +36,19 @@ input:
type: file
description: Index of the annotations file
ontologies: []
- columns:
type: file
description: List of columns in the annotations file, one name per row
ontologies: []
- header_lines:
type: file
description: Contains lines to append to the output VCF header
ontologies: []
- rename_chrs:
type: file
description: Rename annotations according to this file containing "old_name new_name\n"
pairs separated by whitespaces, each on a separate line.
ontologies: []
- columns:
type: file
description: List of columns in the annotations file, one name per row
ontologies: []
- header_lines:
type: file
description: Contains lines to append to the output VCF header
ontologies: []
- rename_chrs:
type: file
description: Rename annotations according to this file containing "old_name new_name\n"
pairs separated by whitespaces, each on a separate line.
ontologies: []
output:
vcf:
- - meta:
Expand Down
4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/bcf.config
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158 changes: 79 additions & 79 deletions modules/nf-core/bcftools/annotate/tests/main.nf.test
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82 changes: 41 additions & 41 deletions modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz"
"test_ann.vcf.gz"
]
],
[
Expand All @@ -19,7 +19,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.csi"
"test_ann.vcf.gz.csi"
]
],
{
Expand All @@ -34,9 +34,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:46:28.350541494"
"timestamp": "2026-02-27T15:29:19.618749659"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": {
"content": [
Expand All @@ -46,7 +46,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
"test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
]
],
[
Expand All @@ -55,7 +55,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.tbi"
"test_ann.vcf.gz.tbi"
]
],
[
Expand All @@ -73,9 +73,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T17:35:23.346991616"
"timestamp": "2026-02-27T15:28:43.350060834"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": {
"content": [
Expand All @@ -85,7 +85,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
"test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
]
],
[
Expand All @@ -97,7 +97,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.csi"
"test_ann.vcf.gz.csi"
]
],
{
Expand All @@ -112,9 +112,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T17:35:15.126643898"
"timestamp": "2026-02-27T15:28:36.101003418"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": {
"content": [
Expand All @@ -124,7 +124,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz"
"test_ann.vcf.gz"
]
],
[
Expand All @@ -133,7 +133,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.tbi"
"test_ann.vcf.gz.tbi"
]
],
[
Expand All @@ -151,9 +151,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:46:46.844515012"
"timestamp": "2026-02-27T15:29:34.19449127"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": {
"content": [
Expand All @@ -163,7 +163,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz"
"test_ann.vcf.gz"
]
],
[
Expand All @@ -175,7 +175,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.csi"
"test_ann.vcf.gz.csi"
]
],
{
Expand All @@ -190,9 +190,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:46:37.561478889"
"timestamp": "2026-02-27T15:29:26.927815399"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": {
"content": [
Expand All @@ -202,7 +202,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
"test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9"
]
],
[
Expand All @@ -214,7 +214,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.csi"
"test_ann.vcf.gz.csi"
]
],
{
Expand All @@ -229,9 +229,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T17:35:06.608740206"
"timestamp": "2026-02-27T15:28:28.891823681"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": {
"content": [
Expand All @@ -241,7 +241,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz"
"test_ann.vcf.gz"
]
],
[
Expand All @@ -262,9 +262,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:46:18.623176402"
"timestamp": "2026-02-27T15:29:12.400301681"
},
"sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output": {
"content": [
Expand Down Expand Up @@ -295,9 +295,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:57:59.109447684"
"timestamp": "2026-02-27T15:28:50.375384421"
},
"sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": {
"content": [
Expand All @@ -307,7 +307,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d"
"test_ann.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d"
]
],
[
Expand All @@ -328,9 +328,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T17:34:58.100296619"
"timestamp": "2026-02-27T15:28:21.320211288"
},
"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": {
"content": [
Expand All @@ -340,7 +340,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d"
"test_ann.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d"
]
],
[
Expand All @@ -361,9 +361,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T17:34:49.49779004"
"timestamp": "2026-02-27T15:28:13.274072987"
},
"sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": {
"content": [
Expand All @@ -373,7 +373,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz"
"test_ann.vcf.gz"
]
],
[
Expand All @@ -385,7 +385,7 @@
"id": "test",
"single_end": false
},
"test_vcf.vcf.gz.csi"
"test_ann.vcf.gz.csi"
]
],
{
Expand All @@ -400,9 +400,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:58:16.686295153"
"timestamp": "2026-02-27T15:29:05.094685409"
},
"sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output": {
"content": [
Expand Down Expand Up @@ -433,8 +433,8 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
"nextflow": "25.10.3"
},
"timestamp": "2026-01-15T16:58:07.908352766"
"timestamp": "2026-02-27T15:28:57.906382655"
}
}
4 changes: 4 additions & 0 deletions modules/nf-core/bcftools/annotate/tests/nextflow.config
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@@ -0,0 +1,4 @@
process {
ext.args = "${params.args_modules}"
ext.prefix = { "${meta.id}_ann" }
}
4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/vcf.config
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4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config
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4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config
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4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config
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6 changes: 2 additions & 4 deletions modules/nf-core/bcftools/merge/main.nf
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Expand Up @@ -8,10 +8,8 @@ process BCFTOOLS_MERGE {
: 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}"

input:
tuple val(meta), path(vcfs), path(tbis)
tuple val(meta2), path(fasta)
tuple val(meta3), path(fai)
tuple val(meta4), path(bed)
tuple val(meta), path(vcfs), path(tbis), path(bed)
tuple val(meta2), path(fasta), path(fai)

output:
tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf
Expand Down
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