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Fix call to SENTIEON_DEDUP #1465

Merged
merged 2 commits into from
Apr 15, 2024
Merged

Fix call to SENTIEON_DEDUP #1465

merged 2 commits into from
Apr 15, 2024

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asp8200
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@asp8200 asp8200 commented Apr 15, 2024

I got:

ERROR ~ Error executing process > 'NFCORE_SAREK:sarek:BAM_SENTIEON_DEDUP:SENTIEON_DEDUP (1)'

Caused by:
  Not a valid path value type: java.util.LinkedHashMap ([id:genome])

on

nextflow run main.nf -profile test_cache,sentieon_dedup_bam,singularity --outdir results  -c ngc_pbs.config

Fix tested manually.

https://nfcore.slack.com/archives/C05V9FRJYMV/p1713173654428819?thread_ts=1713164739.053059&cid=C05V9FRJYMV

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/sarek 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>).
  • 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).

@asp8200 asp8200 changed the base branch from master to dev April 15, 2024 10:14
@nf-core nf-core deleted a comment from github-actions bot Apr 15, 2024
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github-actions bot commented Apr 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dd0176e

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.1
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-15 10:19:12

@asp8200 asp8200 marked this pull request as ready for review April 15, 2024 10:17
@asp8200 asp8200 requested review from maxulysse and removed request for maxulysse April 15, 2024 10:18
kenibrewer
kenibrewer approved these changes Apr 15, 2024
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Nice find!

@maxulysse maxulysse merged commit aaf2151 into nf-core:dev Apr 15, 2024
21 checks passed
@asp8200 asp8200 deleted the fix_subworkflow_BAM_SENTIEON_DEDUP branch June 4, 2024 10:49
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@kenibrewer kenibrewer kenibrewer approved these changes

@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@asp8200 @maxulysse @kenibrewer @edmundmiller