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FIX: update modules #1227

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merged 4 commits into from
Sep 12, 2023
Merged

FIX: update modules #1227

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fa0633d
update CHANGELOG
maxulysse Sep 12, 2023
545a2ac
fix lint warning
maxulysse Sep 12, 2023
d4c9d19
update modules
maxulysse Sep 12, 2023
7bebb39
fix lint warning
maxulysse Sep 12, 2023
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1 change: 1 addition & 0 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ repository_type: pipeline
lint:
actions_ci: False
files_exist:
- .github/workflows/awsfulltest.yml
- conf/modules.config
files_unchanged:
- assets/nf-core-sarek_logo_light.png
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -36,6 +36,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1200](https://github.com/nf-core/sarek/pull/1200) - Streamline Github Actions workflows
- [#1212](https://github.com/nf-core/sarek/pull/1212) - Use matrix for AWS megatests
- [#1218](https://github.com/nf-core/sarek/pull/1218) - Remove Singularity tests for GHA
- [#1227](https://github.com/nf-core/sarek/pull/1227) - Update modules

### Fixed

Expand Down Expand Up @@ -67,6 +68,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1222](https://github.com/nf-core/sarek/pull/1222) - Better documentation for annotation cache
- [#1224](https://github.com/nf-core/sarek/pull/1224) - Update BCFTOOLS_SORT module with `--temp-dir .` added as option, which was required for Singularity
- [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests
- [#1227](https://github.com/nf-core/sarek/pull/1227) - Lint warning fix

### Dependencies

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6 changes: 3 additions & 3 deletions modules.json
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Expand Up @@ -32,7 +32,7 @@
},
"bwa/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
"installed_by": ["modules"]
},
"bwa/mem": {
Expand All @@ -42,7 +42,7 @@
},
"bwamem2/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
"installed_by": ["modules"]
},
"bwamem2/mem": {
Expand Down Expand Up @@ -102,7 +102,7 @@
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
"installed_by": ["modules"]
},
"deepvariant": {
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16 changes: 9 additions & 7 deletions modules/nf-core/bwa/index/main.nf
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15 changes: 9 additions & 6 deletions modules/nf-core/bwamem2/index/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf
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1 change: 1 addition & 0 deletions nextflow_schema.json
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Expand Up @@ -34,6 +34,7 @@
},
"input_restart": {
"type": "string",
"description": "Automatic retrieval for restart",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
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