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Shigapass #6636

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@maxlcummins maxlcummins commented Sep 13, 2024 •
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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 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

@maxlcummins maxlcummins requested a review from a team as a code owner September 13, 2024 02:20
@maxlcummins maxlcummins requested review from SPPearce and removed request for a team September 13, 2024 02:20
maxlcummins added a commit to maxlcummins/modules that referenced this pull request Sep 16, 2024
@maxlcummins
add main.nf.test.snap and update main.nf.test as per pull request nf-…
5fd2db1 
…core#6636
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If you ask on the nf-core slack github-invitations channel you can be added to the organisation and then the tests will run.

SPPearce
SPPearce approved these changes Sep 20, 2024
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modules/nf-core/shigapass/main.nf Outdated Show resolved Hide resolved
maxlcummins added a commit to maxlcummins/modules that referenced this pull request Sep 24, 2024
@maxlcummins
add main.nf.test.snap and update main.nf.test as per pull request nf-…
418fdb2 
…core#6636
@maxlcummins
Add variable output tolerance for shigapass
a623172 
Shigella flexneri genomes will result in an extra output - fixed the module to handle this
@maxlcummins
Update Shigapass main.nf
826c3bd 
Change shigapass module output delimiter to tab from semicolon
@maxlcummins
Merge branch 'nf-core:master' into shigapass
bc6e41d
SPPearce
SPPearce approved these changes Oct 31, 2024
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Just some minor comments.

modules/nf-core/shigapass/main.nf Outdated
Comment on lines 14 to 15
tuple val(meta), path("*.csv"), emit: report
tuple val(meta), path("*_ShigaPass_summary.csv"), emit: report
tuple val(meta), path("*_ShigaPass_Flex_summary.csv"), optional: true, emit: flex_csv
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Can you please line up the commas (I'd swap the emit before the optional too)

modules/nf-core/shigapass/main.nf
tuple val(meta), path(fasta)

output:
tuple val(meta), path("${prefix}.tsv"), emit: report
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Can you align the commands please (and I would put the optional: true after the emit:)

modules/nf-core/shigapass/main.nf
Comment on lines +46 to +47
# Convert to tab delimited and move to the pwd
sed 's/;/\t/g' ${prefix}/ShigaPass_summary.csv > ${prefix}.tsv
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Why are you converting to tab delimited from csv?

modules/nf-core/shigapass/meta.yml
@@ -0,0 +1,41 @@
name: shigapass
description: ShigaPass is a new in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.
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Suggested change
description: ShigaPass is a new in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.
description: ShigaPass is an in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.

modules/nf-core/shigapass/meta.yml
- stec
tools:
- shigapass:
description: ShigaPass is a new in silico tool used to predict Shigella serotypes
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Suggested change
description: ShigaPass is a new in silico tool used to predict Shigella serotypes
description: ShigaPass is an in silico tool used to predict Shigella serotypes

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@SPPearce SPPearce SPPearce approved these changes

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@maxlcummins @SPPearce