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New module svtypersso #5311

Merged
merged 2 commits into from
Mar 20, 2024
Merged

New module svtypersso #5311

merged 2 commits into from
Mar 20, 2024

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tstoeriko
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PR checklist

Closes #2808

  • 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
  • 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

@tstoeriko tstoeriko requested a review from a team as a code owner March 20, 2024 10:31
@tstoeriko tstoeriko requested review from Aratz and removed request for a team March 20, 2024 10:31
itrujnara
itrujnara approved these changes Mar 20, 2024
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@itrujnara itrujnara left a comment

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Very nice! There are some minor formatting issues, but once you address them you can merge.

modules/nf-core/svtyper/svtypersso/main.nf
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def vcf = vcf ? "--input_vcf ${vcf}" : ""
def fasta = fasta ? "--ref_fasta ${fasta}" : ""
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Align equal signs

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Thanks, fixed it!

modules/nf-core/svtyper/svtypersso/main.nf

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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Align equal signs

@tstoeriko
Adjust formatting
fa87ed1 
- align equal signs
@itrujnara
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Looks good to me, merge when ready

@tstoeriko tstoeriko added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit 4685ac9 Mar 20, 2024
26 checks passed
@tstoeriko tstoeriko deleted the svtypersso branch March 20, 2024 13:19
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
f01d48c 
* master:
  Tcoffee tcs (nf-core#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
  New module svtypersso (nf-core#5311)
jvfe added a commit that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
a2bedc0 
* master:
  Add module nanofilt (#5290)
  Tcoffee tcs (#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (#5302)
  New module svtypersso (#5311)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@tstoeriko @tucano
New module svtypersso (nf-core#5311)
bad2110 
* Add module svtypersso

* Adjust formatting

- align equal signs
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@tstoeriko @jennylsmith
New module svtypersso (nf-core#5311)
699530f 
* Add module svtypersso

* Adjust formatting

- align equal signs
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@tstoeriko
New module svtypersso (nf-core#5311)
b4365a2 
* Add module svtypersso

* Adjust formatting

- align equal signs
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@itrujnara itrujnara itrujnara approved these changes

@Aratz Aratz Awaiting requested review from Aratz Aratz was automatically assigned from nf-core/nf-test

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new module: svtypersso
2 participants
@tstoeriko @itrujnara