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More tests for subworkflows #713

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f18767d
move qc bam to folder
ramprasadn Jul 9, 2025
3b1edbf
move call_repeat_expansions to a folder
ramprasadn Jul 9, 2025
761a80c
rename to main.nf
ramprasadn Jul 9, 2025
e7bd071
update modules
ramprasadn Jul 9, 2025
7ab61c2
add test for qc bam
ramprasadn Jul 10, 2025
c68b73c
add test for call repeat expansions
ramprasadn Jul 10, 2025
6138d67
repeat expansions test
ramprasadn Jul 10, 2025
8abca7d
fix lint
ramprasadn Jul 10, 2025
986f6ad
update snaps
ramprasadn Jul 10, 2025
0ea711c
Merge branch 'dev' of github.com:nf-core/raredisease into test_qc_bam…
ramprasadn Oct 14, 2025
7ccdccf
review suggestions
ramprasadn Oct 14, 2025
4bec5e8
update snaps
ramprasadn Oct 14, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717)
- Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713)

### `Changed`

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1 change: 1 addition & 0 deletions conf/modules/qc_bam.config
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Expand Up @@ -55,6 +55,7 @@ process {
}

withName: '.*QC_BAM:MOSDEPTH' {
ext.args = "--d4"
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ext.prefix = { "${meta.id}_mosdepth" }
}

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38 changes: 19 additions & 19 deletions modules.json
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Expand Up @@ -27,12 +27,12 @@
},
"bcftools/norm": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"bcftools/reheader": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"bcftools/roh": {
Expand Down Expand Up @@ -102,7 +102,7 @@
},
"chromograph": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"cnvnator/cnvnator": {
Expand Down Expand Up @@ -149,7 +149,7 @@
},
"expansionhunter": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"fastp": {
Expand Down Expand Up @@ -305,7 +305,7 @@
},
"mosdepth": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"multiqc": {
Expand All @@ -315,7 +315,7 @@
},
"ngsbits/samplegender": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"peddy": {
Expand All @@ -330,17 +330,17 @@
},
"picard/collecthsmetrics": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/collectwgsmetrics": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/liftovervcf": {
Expand All @@ -355,7 +355,7 @@
},
"picard/renamesampleinvcf": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/sortvcf": {
Expand All @@ -365,7 +365,7 @@
},
"qualimap/bamqc": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"rhocall/annotate": {
Expand Down Expand Up @@ -395,7 +395,7 @@
},
"samtools/index": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/merge": {
Expand All @@ -405,7 +405,7 @@
},
"samtools/sort": {
"branch": "master",
"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/stats": {
Expand Down Expand Up @@ -455,7 +455,7 @@
},
"sentieon/wgsmetrics": {
"branch": "master",
"git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"smncopynumbercaller": {
Expand All @@ -475,7 +475,7 @@
},
"svdb/merge": {
"branch": "master",
"git_sha": "95185f269ec10a33cde61d294fcd4ba7c66bc6b8",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"svdb/query": {
Expand All @@ -495,12 +495,12 @@
},
"tabix/tabix": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"tiddit/cov": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"tiddit/sv": {
Expand All @@ -510,7 +510,7 @@
},
"ucsc/wigtobigwig": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"untar": {
Expand All @@ -535,7 +535,7 @@
},
"verifybamid/verifybamid2": {
"branch": "master",
"git_sha": "33278f733f3452dc77bde5c1a45db3a5f9278ac0",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
}
}
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4 changes: 3 additions & 1 deletion modules/nf-core/bcftools/norm/environment.yml
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18 changes: 11 additions & 7 deletions modules/nf-core/bcftools/norm/main.nf
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30 changes: 19 additions & 11 deletions modules/nf-core/bcftools/norm/meta.yml
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