Open
Conversation
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>
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>
11 tasks
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>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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:
Outputs:
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda