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Merged
Lukecele merged 10 commits into from
Oct 1, 2026
Merged

abra2: fix index output pattern #13039

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bc69129
abra2: fix index output pattern
Lukecele Sep 28, 2026
369723a
Merge branch 'master' into fix/abra2-index-output
Lukecele Sep 28, 2026
51e86d5
Merge branch 'master' into fix/abra2-index-output
famosab Sep 29, 2026
61b903d
Merge branch 'master' into fix/abra2-index-output
Lukecele Sep 29, 2026
fd8a2ce
Merge branch 'master' into fix/abra2-index-output
famosab Sep 30, 2026
3b42f0f
fix(abra2): make index snapshots profile independent
Lukecele Sep 30, 2026
abed64b
Merge branch 'master' into fix/abra2-index-output
Lukecele Sep 30, 2026
466bb1b
Merge branch 'master' into fix/abra2-index-output
Lukecele Sep 30, 2026
0661dc1
fix(abra2): align stub index filename with real output
Lukecele Sep 30, 2026
898d966
Merge branch 'master' into fix/abra2-index-output
Lukecele Oct 1, 2026
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4 changes: 2 additions & 2 deletions modules/nf-core/abra2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ process ABRA2 {

output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.bam.bai"), emit: bai, optional: true
tuple val(meta), path("*.bai"), emit: bai, optional: true
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tuple val("${task.process}"), val('abra2'), eval("abra2 2>&1 | sed -n 's/.*Abra version: //p'"), topic: versions, emit: versions_abra2

when:
Expand Down Expand Up @@ -49,6 +49,6 @@ process ABRA2 {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.abra.bam
touch ${prefix}.abra.bam.bai
touch ${prefix}.abra.bai
"""
}
4 changes: 2 additions & 2 deletions modules/nf-core/abra2/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -111,10 +111,10 @@ output:
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.bam.bai":
- "*.bai":
type: file
description: BAM index file (optional)
pattern: "*.abra.bam.bai"
pattern: "*.bai"
ontologies:
- edam: "http://edamontology.org/format_3327"
versions_abra2:
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/abra2/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match()}
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"], unstableKeys:["bai"])).match()}
)
}

Expand Down Expand Up @@ -74,7 +74,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match()}
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"], unstableKeys:["bai"])).match()}
)
}

Expand Down Expand Up @@ -147,7 +147,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match()}
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"], unstableKeys:["bai"])).match()}
)
}

Expand Down Expand Up @@ -187,7 +187,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match()}
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"], unstableKeys:["bai"])).match()}
)
}

Expand Down Expand Up @@ -240,7 +240,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"])).match()}
{ assert snapshot(sanitizeOutput(process.out, readsMD5Keys:["bam"], unstableKeys:["bai"])).match()}
)
}
}
Expand Down
69 changes: 51 additions & 18 deletions modules/nf-core/abra2/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,13 @@
"content": [
{
"bai": [

[
{
"id": "test_known_indels",
"single_end": false
},
"test_known_indels.test.paired_end.sorted.bai"
]
],
"bam": [
[
Expand All @@ -23,10 +29,10 @@
]
}
],
"timestamp": "2026-08-25T12:57:32.113637",
"timestamp": "2026-09-29T22:12:20.762243403",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
},
"sarscov2 - bam - stub": {
Expand All @@ -38,7 +44,7 @@
"id": "test",
"single_end": false
},
"test.abra.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.abra.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"bam": [
Expand All @@ -59,17 +65,23 @@
]
}
],
"timestamp": "2026-08-25T15:10:45.755991",
"timestamp": "2026-10-01T01:48:32.279961685",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
},
"homo_sapiens - rnaseq - with_gtf": {
"content": [
{
"bai": [

[
{
"id": "test_rnaseq",
"single_end": false
},
"test_rnaseq.test.rna.paired_end.sorted.bai"
]
],
"bam": [
[
Expand All @@ -89,17 +101,23 @@
]
}
],
"timestamp": "2026-08-25T12:56:58.237748",
"timestamp": "2026-09-29T22:11:57.224746065",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
},
"sarscov2 - bam": {
"content": [
{
"bai": [

[
{
"id": "test",
"single_end": false
},
"test.test.paired_end.sorted.bai"
]
],
"bam": [
[
Expand All @@ -119,17 +137,23 @@
]
}
],
"timestamp": "2026-08-25T12:56:21.647038",
"timestamp": "2026-09-29T22:11:21.675183586",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
},
"sarscov2 - bam - with_targets": {
"content": [
{
"bai": [

[
{
"id": "test",
"single_end": false
},
"test.test.paired_end.sorted.bai"
]
],
"bam": [
[
Expand All @@ -149,17 +173,26 @@
]
}
],
"timestamp": "2026-08-25T12:56:34.804912",
"timestamp": "2026-09-29T22:11:32.847963121",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
},
"homo_sapiens - multiple_bams": {
"content": [
{
"bai": [

[
{
"id": "test_multi",
"single_end": false
},
[
"test_multi.test.paired_end.sorted.bai",
"test_multi.test2.paired_end.sorted.bai"
]
]
],
"bam": [
[
Expand All @@ -182,10 +215,10 @@
]
}
],
"timestamp": "2026-08-25T15:11:18.053315",
"timestamp": "2026-09-29T22:12:09.148921831",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
"nextflow": "25.10.2"
}
}
}
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