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Add bwameme #553

Merged
merged 7 commits into from
May 21, 2024
Merged

Add bwameme #553

merged 7 commits into from
May 21, 2024

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ramprasadn
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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!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented May 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bd01ffd

+| ✅ 183 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • 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
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-21 12:19:26

@ramprasadn ramprasadn marked this pull request as ready for review May 19, 2024 19:20
jemten
jemten reviewed May 20, 2024
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Looks good
Could you also update the metromap to include meme?

conf/modules/align_MT.config Show resolved Hide resolved
conf/modules/align_MT.config Show resolved Hide resolved
subworkflows/local/align.nf Outdated
@@ -40,11 +42,12 @@ workflow ALIGN {
ch_fastp_json = FASTP.out.json
}

if (params.aligner.equals("bwamem2") || params.aligner.equals("bwa")) {
ALIGN_BWA_BWAMEM2 ( // Triggered when params.aligner is set as bwamem2 or bwa
if (params.aligner.equals("bwamem2") || params.aligner.equals("bwa") || params.aligner.equals("bwameme")) {
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Suggested change
if (params.aligner.equals("bwamem2") || params.aligner.equals("bwa") || params.aligner.equals("bwameme")) {
if (params.aligner.matches("bwamem2| bwa|bwameme")) {

just a little shorter

@ramprasadn ramprasadn requested a review from jemten May 21, 2024 12:40
jemten
jemten approved these changes May 21, 2024
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Looks good!

@ramprasadn ramprasadn merged commit 5ec2692 into dev May 21, 2024
6 checks passed
@ramprasadn ramprasadn deleted the addbwameme branch May 28, 2024 08:24
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten