CellRanger Multi => add to MultiQC report

[nick-youngblut]

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]

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.