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add nf-test to samtools/faidx - #3936 #5177

Merged
merged 4 commits into from
Mar 18, 2024
Merged

add nf-test to samtools/faidx - #3936 #5177

merged 4 commits into from
Mar 18, 2024

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vlebars
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@vlebars vlebars commented Mar 18, 2024

PR checklist

Add nf-test to samtools/faidx

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@vlebars vlebars self-assigned this Mar 18, 2024
@vlebars vlebars requested a review from a team as a code owner March 18, 2024 12:10
LouisLeNezet
LouisLeNezet reviewed Mar 18, 2024
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Need to figure out why the extract.fa is not generated with the nextflow.config

@vlebars vlebars added this pull request to the merge queue Mar 18, 2024
Merged via the queue into nf-core:master with commit aeb02a3 Mar 18, 2024
18 checks passed
@vlebars vlebars deleted the samtools_faidx_test branch March 18, 2024 15:59
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@vlebars @LouisLeNezet @tucano
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
a9cc5d8 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@vlebars @LouisLeNezet @jennylsmith
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
9dc88ed 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@vlebars @LouisLeNezet
add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)
37a8f02 
* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>
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@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

@phue phue Awaiting requested review from phue

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@vlebars @LouisLeNezet