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Fix rrbs and skip_dedup publishing #583

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Merged
sateeshperi merged 4 commits into from
Dec 8, 2025
Merged

Fix rrbs and skip_dedup publishing #583

sateeshperi merged 4 commits into from
Dec 8, 2025

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@sateeshperi sateeshperi commented Dec 7, 2025

closes #579 and also fix bwamem publishing

@sateeshperi
fix: add BWA_INDEX and SAMTOOLS_IDXSTATS processes, update publishDir…
6fdd85a 
… settings

- Introduced new configuration for BWA_INDEX to manage reference genome output.
- Added SAMTOOLS_IDXSTATS process for generating index statistics.
- Updated publishDir settings in existing processes to accommodate deduplication and RRBS parameters.
- Enhanced documentation to reflect new output structure and file descriptions.
@sateeshperi
chore: update test snapshots after skip_dedup/rrbs publishing fix
c2caad7
@sateeshperi sateeshperi requested a review from a team as a code owner December 7, 2025 06:29
@sateeshperi
chore: update changelog for correct bam file publishing in alignments…
10e48fd 
… folder for --skip_deduplication and --rrbs options
@sateeshperi sateeshperi requested review from eduard-watchmaker and removed request for a team and FelixKrueger December 7, 2025 06:31
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github-actions bot commented Dec 7, 2025 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit e56eb61

+| ✅ 234 tests passed       |+
#| ❔   7 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-07 18:59:11

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sateeshperi commented Dec 7, 2025

@eduard-watchmaker kindly pull down this branch and run bwamem test profile and confirm if all the output files are there and in expected locations.

Also if you could bump the gpu snapshot while at it, that would be great. Thanks

@sateeshperi sateeshperi linked an issue Dec 7, 2025 that may be closed by this pull request
--rrbs samtools sort bam incorrectly named with deduplicated prefix #579
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eduard-watchmaker
eduard-watchmaker reviewed Dec 7, 2025
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eduard-watchmaker approved these changes Dec 8, 2025
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All looks good, I did a real run and checked that all files are there and named as reported on the output.md file

@sateeshperi sateeshperi merged commit 04f4e35 into dev Dec 8, 2025
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@sateeshperi sateeshperi deleted the fix-publishing branch December 8, 2025 01:32
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--rrbs samtools sort bam incorrectly named with deduplicated prefix

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