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Change hardcoded platform value to params.platform in modules/align_MT.config #475

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merged 3 commits into from
Jan 12, 2024
Merged

Change hardcoded platform value to params.platform in modules/align_MT.config #475

merged 3 commits into from
Jan 12, 2024

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alkc
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@alkc alkc commented Jan 11, 2024 •
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Tiny update that sets a hardcoded platform value in the ALIGN_MT.config to use params.platform instead.

Compare with the config for the equivalent ALIGN_MT_SHIFT process:

raredisease/conf/modules/align_MT.config

Lines 89 to 97 in a2e6812

withName: '.*ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT' {
ext.args = { [
"--VALIDATION_STRINGENCY LENIENT",
"--RGLB lib",
"--RGPL ${params.platform}",
"--RGPU barcode",
"--RGSM ${meta.id}"
].join(' ').trim() }
}

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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github-actions bot commented Jan 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d07ddd6

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-12 04:17:43

@alkc alkc changed the title Change hardcoded platform value to params.platform Change hardcoded platform value to params.platform in modules/align_MT.config Jan 11, 2024
jemten
jemten approved these changes Jan 11, 2024
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Good catch @alkc!

ramprasadn
ramprasadn requested changes Jan 11, 2024
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Should be changed here as well?

raredisease/conf/modules/align_MT.config

Line 45 in a2e6812

"--RGPL ILLUMINA",

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alkc commented Jan 11, 2024

Should be changed here as well?

raredisease/conf/modules/align_MT.config

Line 45 in a2e6812

"--RGPL ILLUMINA",

That's the line changed by this PR!

See: 0809a40

@alkc alkc requested a review from ramprasadn January 11, 2024 22:28
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ramprasadn commented Jan 12, 2024 •
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Gah.. sorry! My brain had a paralysis for a second there 😅

@ramprasadn ramprasadn merged commit e5734fc into nf-core:dev Jan 12, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

@jemten jemten jemten approved these changes

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@alkc @ramprasadn @jemten