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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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CellRanger Multi => add to MultiQC report #377

Open nick-youngblut opened 1 month ago

nick-youngblut commented 1 month ago

Description of feature

At least for v2.7.1, the output reports created by cellranger multi are not included in the final MultiQC report.

My command:

nextflow run main.nf \
  --aligner cellrangermulti \
  --skip_cellrangermulti_vdjref \
  --skip_emptydrops \
  --gex_frna_probe_set Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv \
  --cellranger_multi_barcodes sample_barcodes.csv \
  --cellranger_index refdata-gex-GRCh38-2020-A/ \
  --input samples.csv \
  --outdir scrnaseq_output

The MultiQC report only includes the fastqc results.

nick-youngblut commented 1 month ago

Also, the cellrangermulti output directory is a bit chaotic, since it includes per-sample output and combined output in the same directory. So, if the user has many samples, it can be hard to find the non-sample directories (e.g., mkgtf, mtx_conversions, or count) among all of the sample directories.

grst commented 3 weeks ago

Depends on https://github.com/MultiQC/MultiQC/pull/2861