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Udate GATK modules - Fix output line lack of specificity #1839

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Udate GATK modules - Fix output line lack of specificity #1839

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5fe5cdf
Release 3.5.1 (#1799)
maxulysse Feb 18, 2025
0d7c46e
applybqsr updated
johnoooh Mar 18, 2025
3af46bc
Fix modules.json
johnoooh Mar 24, 2025
42cabd7
updating gatk modules
johnoooh Mar 24, 2025
af50f23
updating gatk modules
johnoooh Mar 24, 2025
d6d2b5e
Merge branch 'bugfix/applybqsr_outfile' of github.com:johnoooh/sarek …
johnoooh Mar 24, 2025
826a7ae
Update CHANGELOG.md
johnoooh Mar 24, 2025
1b64724
Update multiqc_config.yml
johnoooh Mar 24, 2025
0b4e798
merge markers removed
johnoooh Mar 24, 2025
b54919a
Update modules.json
johnoooh Mar 24, 2025
7ffb226
Update main.nf
johnoooh Mar 24, 2025
48d13d5
base recalibrator
johnoooh Mar 24, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1806](https://github.com/nf-core/sarek/pull/1806) - Use `nft-vcf` for nf-test vcf assertions
- [1814](https://github.com/nf-core/sarek/pull/1814) - Added link to Bluesky
- [1829](https://github.com/nf-core/sarek/pull/1829) - Add muse as variant caller to images
- [1835](https://github.com/nf-core/sarek/pull/1835) - Add GPU testing possibilities

#### Changed

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1 change: 1 addition & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -3,6 +3,7 @@ custom_logo_url: https://github.com/nf-core/sarek/
custom_logo_title: "nf-core/sarek"

report_comment: >

This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev"
target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to
interpret these results, please see the <a href="https://nf-co.re/sarek/dev/docs/output"
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48 changes: 24 additions & 24 deletions modules.json
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Expand Up @@ -181,7 +181,7 @@
},
"gatk4/applybqsr": {
"branch": "master",
"git_sha": "6b3bf38285d94cc1ea3cd9fa93310d54b04c3819",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/applyvqsr": {
Expand All @@ -191,118 +191,118 @@
},
"gatk4/baserecalibrator": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/calculatecontamination": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/cnnscorevariants": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/estimatelibrarycomplexity": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/filtermutectcalls": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/filtervarianttranches": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/gatherbqsrreports": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/gatherpileupsummaries": {
"branch": "master",
"git_sha": "679f45cae4f603f12d7c38c042afee11150574a0",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/genomicsdbimport": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/genotypegvcfs": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/getpileupsummaries": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/intervallisttobed": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"],
"patch": "modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff"
},
"gatk4/learnreadorientationmodel": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/markduplicates": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/mergemutectstats": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/mergevcfs": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/mutect2": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4/variantrecalibrator": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4spark/applybqsr": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "2b7eb9b3fae57cfaa2559b47e7eff855a81978ac",
"installed_by": ["modules"]
},
"gatk4spark/baserecalibrator": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gatk4spark/markduplicates": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gawk": {
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6 changes: 5 additions & 1 deletion modules/nf-core/gatk4/applybqsr/environment.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/gatk4/applybqsr/main.nf
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56 changes: 28 additions & 28 deletions modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap
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6 changes: 5 additions & 1 deletion modules/nf-core/gatk4/baserecalibrator/environment.yml
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14 changes: 7 additions & 7 deletions modules/nf-core/gatk4/baserecalibrator/main.nf
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