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Add new module: qcatch#10032

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an-altosian wants to merge 9 commits intonf-core:masterfrom
an-altosian:qcatch
Open

Add new module: qcatch#10032
an-altosian wants to merge 9 commits intonf-core:masterfrom
an-altosian:qcatch

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@an-altosian an-altosian commented Feb 13, 2026

QCatch is a quality control and cell filtering tool for single-cell RNA-seq data processed by alevin-fry. It generates comprehensive QC reports and filtered count matrices.

Inputs:

  • meta: sample metadata map
  • chemistry: chemistry type (10X_3p_v2, 10X_3p_v3, 10X_3p_v4, 10X_5p_v3, 10X_3p_LT, 10X_HT)
  • quant_dir: alevin-fry quantification results directory

Outputs:

  • HTML QC report
  • Filtered h5ad file
  • Metrics summary CSV
  • versions.yml

PR checklist

Closes #XXX

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

QCatch is a quality control and cell filtering tool for single-cell RNA-seq
data processed by alevin-fry. It generates comprehensive QC reports and
filtered count matrices.

Inputs:
- meta: sample metadata map
- chemistry: chemistry type (10X_3p_v2, 10X_3p_v3, 10X_3p_v4, 10X_5p_v3, 10X_3p_LT, 10X_HT)
- quant_dir: alevin-fry quantification results directory

Outputs:
- HTML QC report
- Filtered h5ad file
- Metrics summary CSV
- versions.yml

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
an-altosian and others added 5 commits February 13, 2026 22:30
Add MPLCONFIGDIR and TMPDIR environment exports to redirect matplotlib
config writes to the working directory. This fixes Singularity test
failures where home directory is mounted read-only.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Scanpy uses numba for compiled functions, which requires a writable
cache directory. In Singularity, the default cache location inside
the container is read-only.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add additional environment variables commonly used alongside
NUMBA_CACHE_DIR to ensure full compatibility with Singularity:
- NUMBA_DISABLE_CACHE=1: Disables numba caching entirely
- XDG_CACHE_HOME: Redirects XDG cache to working directory

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
an-altosian and others added 3 commits February 14, 2026 14:49
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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2 participants