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Centrifuger quant#11234

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haris18s:centrifuger_quant
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Centrifuger quant#11234
haris18s wants to merge 4 commits intonf-core:masterfrom
haris18s:centrifuger_quant

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@haris18s haris18s commented Apr 20, 2026

PR checklist

Closes #XXX

  • [x ] This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • [x ] If you've added a new tool - have you followed the module conventions in the contribution docs
  • [x ] If necessary, include test data in your PR.
  • [x ] Remove all TODO statements.
  • [x ] Broadcast software version numbers to topic: versions - See version_topics
  • [x ] Follow the naming conventions.
  • [x ] Follow the parameters requirements.
  • [x ] Follow the input/output options guidelines.
  • [x ] Add a resource label
  • [x ] 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

Description

Add new module for centrifuger-quant — taxonomic quantification/profiling from Centrifuger classification results.

Module details

  • Tool: Centrifuger v1.1.0 (centrifuger-quant)
  • Inputs: Classification TSV file (from centrifuger/centrifuger module) + Centrifuger database (.cfr files)
  • Outputs: Taxonomic profiling report TSV, version info
  • Depends on: centrifuger/centrifuger module (classification) and centrifuger/build module (database building)

mashehu
mashehu reviewed Apr 20, 2026
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Comment thread modules/nf-core/centrifuger/centrifuger/tests/main.nf.test
mashehu
mashehu reviewed Apr 20, 2026
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Comment thread modules/nf-core/centrifuger/centrifuger/main.nf
mashehu
mashehu reviewed Apr 20, 2026
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Comment thread modules/nf-core/centrifuger/centrifuger/main.nf
@haris18s haris18s force-pushed the centrifuger_quant branch from d084a2f to f33e66e Compare April 22, 2026 15:27
sofstam
sofstam reviewed Apr 23, 2026
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Comment thread modules/nf-core/centrifuger/centrifuger/main.nf
Comment thread modules/nf-core/centrifuger/centrifuger/main.nf
def unclassified_arg = save_unclassified ? "--un ${prefix}.unclassified" : ""
def classified_arg = save_classified ? "--cl ${prefix}.classified" : ""
def barcode_arg = barcode ? "--barcode ${barcode}" : ""
def umi_arg = umi ? "--UMI ${umi}" : ""
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@sofstam sofstam Apr 23, 2026

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--read-format STR: format for read, barcode and UMI files, e.g. r1:0:-1,r2:0:-1,bc:0:15,um:16:-1 for paired-end files with barcode and UMI

This might be needed too.

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@haris18s haris18s Apr 24, 2026

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i think they can pass through args right? is a STR not a file.

Comment thread modules/nf-core/centrifuger/centrifuger/main.nf

"""
echo ${args}
#main output
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@sofstam sofstam Apr 23, 2026

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Do you need this line?

Comment thread modules/nf-core/centrifuger/centrifuger/main.nf
touch ${prefix}.tsv

#Optional outputs
if ${save_unclassified}; then
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@sofstam sofstam Apr 23, 2026

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Maybe the optional outputs can be moved after def prefix

Comment thread modules/nf-core/centrifuger/centrifuger/tests/main.nf.test
Comment thread modules/nf-core/centrifuger/quantification/main.nf
Comment thread modules/nf-core/centrifuger/quantification/main.nf
Comment thread modules/nf-core/centrifuger/quantification/main.nf

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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@sofstam sofstam Apr 23, 2026

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Here as well

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@haris18s haris18s Apr 24, 2026

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you mean to include (when not -x is given) part in stub as well?

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@sofstam sofstam Apr 24, 2026

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yes

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@haris18s haris18s Apr 24, 2026

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I included it you may check, it may be redundant because not used in stub..

Comment thread modules/nf-core/centrifuger/quantification/meta.yml Outdated
Comment thread modules/nf-core/centrifuger/quantification/meta.yml Outdated
@haris18s haris18s force-pushed the centrifuger_quant branch 2 times, most recently from 00f1ce3 to 883c987 Compare April 24, 2026 11:22
@haris18s haris18s force-pushed the centrifuger_quant branch from 883c987 to 598875e Compare April 24, 2026 11:30
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haris18s commented Apr 24, 2026

@jfy133, @sofstam, i think i have resolved comments, take a look please :)

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@haris18s @mashehu @sofstam