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Add new module: qcatch#10032

Merged
DongzeHE merged 21 commits intonf-core:masterfrom
an-altosian:qcatch
Feb 21, 2026
Merged

Add new module: qcatch#10032
DongzeHE merged 21 commits intonf-core:masterfrom
an-altosian:qcatch

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@an-altosian an-altosian commented Feb 13, 2026 •
edited by DongzeHE
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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

@an-altosian @claude
Add new module: qcatch
8823577 
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
@an-altosian @claude
Fix Singularity compatibility for matplotlib config directory
337d346 
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>
@an-altosian @claude
Add NUMBA_CACHE_DIR for Singularity numba caching fix
c86ca4f 
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>
@an-altosian @claude
Add NUMBA_DISABLE_CACHE and XDG_CACHE_HOME for Singularity
4cb85a1 
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>
@an-altosian @claude
Switch to BioContainers for qcatch module
9e0d516 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian @claude
Address PR review: use Seqera Containers, local prefix, wildcard outputs
31e52dd 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian an-altosian mentioned this pull request Feb 14, 2026
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an-altosian and others added 3 commits February 14, 2026 14:49
@an-altosian @claude
Fix lint: update meta.yml outputs, remove hardcoded env vars
1f75971 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian @claude
Move env vars to test config for Singularity compatibility
371169c 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian @claude
Remove unnecessary TMPDIR and XDG_CACHE_HOME from test config
2995baf 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
fmalmeida
fmalmeida reviewed Feb 16, 2026
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an-altosian commented Feb 16, 2026

Thanks for the review, @fmalmeida ! Both of your comments are addressed. Any other thoughts?

an-altosian and others added 2 commits February 16, 2026 17:18
@an-altosian @claude
Use exists() for h5ad snapshot due to non-deterministic gzip output
f187266 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian @claude
Snapshot h5ad file size instead of md5 for deterministic testing
a28e55f 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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an-altosian commented Feb 16, 2026

Ok before we merge, I want to update qcatch version to export a count matrix that is deterministic (row and column sorted by names). If you think there is nothing else wrong, I will merge this PR with the new version today or tomorrow.

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fmalmeida commented Feb 16, 2026

Sounds good! Let me know when.

an-altosian and others added 4 commits February 18, 2026 18:15
@an-altosian @claude
Update qcatch to 0.2.9, use size() for non-deterministic outputs
fa98619 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@DongzeHE
Merge branch 'master' into qcatch
42c25bb
@an-altosian @claude
Fix conda environment.yml pip dependency syntax
4e8ce1a 
Use proper conda pip dependency format (pip: section) instead of
pip:: channel prefix which conda doesn't recognize as a channel.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@an-altosian @claude
Pin pip version in conda environment.yml to satisfy linter
bddfbf9 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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DongzeHE commented Feb 18, 2026 •
edited
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@fmalmeida Done. Please check.

UPDATE: Actually, I need to change one more thing. sorry for the false positive.

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fmalmeida commented Feb 19, 2026

Let me know when :)

an-altosian and others added 2 commits February 21, 2026 17:50
@an-altosian @claude
Update qcatch to 0.2.10 with deterministic h5ad output
f1cb3fc 
- Update qcatch from 0.2.9 to 0.2.10 (fixes non-deterministic layer
  ordering in h5ad files)
- Update Wave container images for 0.2.10
- Use md5 snapshot for h5ad output now that it is deterministic

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@DongzeHE
Merge branch 'master' into qcatch
6aa67f5
@DongzeHE DongzeHE enabled auto-merge February 21, 2026 18:05
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DongzeHE commented Feb 21, 2026

@fmalmeida It is ready from my side!

fmalmeida
fmalmeida approved these changes Feb 21, 2026
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Cool!

@DongzeHE DongzeHE added this pull request to the merge queue Feb 21, 2026
Merged via the queue into nf-core:master with commit 00754db Feb 21, 2026
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