Feat/methylation filtering

[adthrasher]

Add filtering of sex chromosomes to the UMAP generation. Also generate a list of probes that have SNPs.

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• You have added a few sentences describing the PR here.
• The code passes all CI tests without any errors or warnings.
• You have added tests (when appropriate).
• You have added an entry in any relevant CHANGELOGs (when appropriate).
• If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
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[Copilot]

Pull request overview

This PR adds filtering of sex chromosome probes to the UMAP generation pipeline and generates lists of probes that are affected by SNPs or do not map to the genome. The changes enhance the methylation workflow by providing more granular control over probe filtering and making filtered probe lists available as outputs.

Key changes:

• Added sex chromosome probe filtering capability to the UMAP generation
• Generated and output lists of SNP-affected probes and non-genomic probes
• Implemented a batched concatenation mechanism for large probe lists

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
workflows/methylation/methylation-standard.wdl	Added new outputs and batched probe list concatenation logic
workflows/methylation/methylation-preprocess.wdl	Added task to list sex chromosome probes and updated outputs
workflows/methylation/methylation-cohort.wdl	Integrated sex probe filtering into the cohort workflow
workflows/methylation/CHANGELOG.md	Documented new probe list outputs
scripts/methylation/methylation-preprocess.R	Added logic to identify and output SNP-affected and non-genomic probes
scripts/methylation/list-sex-probes.R	New script to generate sex chromosome probe list
scripts/methylation/filter.py	Added support for excluding probes from additional file sources
scripts/CHANGELOG.md	Documented script changes
docker/pandas/package.json	Incremented revision for pandas container
docker/minfi/package.json	Incremented revision for minfi container
docker/minfi/Dockerfile	Added new list-sex-probes.R script to container

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[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

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