Fix: Support for --aligner cellrangerarc

[matbonfanti]

This PR introduces two changes to ensure the pipeline functions correctly when using --aligner cellrangerarc:

• A dedicated parsing section structures the samplesheet channel to be compatible with the cellrangerarc module.
• The raw and filtered gene expression matrices are now extracted from the cellrangerarc module output for further processing in the pipeline.

See issues #389 and #374

Testing

I have tested these changes locally subsampling FASTQ files from 10x Genomics, and the pipeline runs successfully. For reference, here is the samplesheet used in testing:

sample,fastq_1,fastq_2,fastq_barcode,sample_type
10k_PBMC,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L001_R1_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L001_R2_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L001_R3_001.fastq.gz,atac
10k_PBMC,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L002_R1_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L002_R2_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_atac_S2_L002_R3_001.fastq.gz,atac
10k_PBMC,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_gex_S2_L001_R1_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_gex_S2_L001_R2_001.fastq.gz,,gex
10k_PBMC,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_gex_S2_L002_R1_001.fastq.gz,/scratch/matteo.bonfanti/test_scrnaseq/fastqs/10k_PBMC_Multiome_nextgem_Chromium_X_gex_S2_L002_R2_001.fastq.gz,,gex

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[grst]

Hi @matbonfanti,

thanks for working on this!
Would you by any chance also have time to implement a test-case for cellrangerarc? It is currently not covered by CI at all which is one of the reasons the bug you are fixing exists in the first case. See also #290.

[matbonfanti]

Hi @grst, that was indeed the plan!

I have seen that on the test-dataset repo there is already a dataset for atac-seq (https://github.com/nf-core/test-datasets/tree/modules/data/genomics/homo_sapiens/10xgenomics/cellranger-atac) which I think would be a good test, for starters. In the long term I could make a new test using multiome data (atac+gex) that would be probably more appropriate, but it will definitely take much more time to implement.

If you agree, I will start including the atac-only test in this PR, so that atac alignment will be fixed soon in the dev branch. Then maybe I can make a new PR for the other test dataset.