sc tools docker image version update v0.0.39 -> v0.0.41

[michael-kotliar]

Changes:

1. All Seurat based workflows export the log into HTML format with embedded plots
2. All clustering workflows (RNA, ATAC, WNN) now also support resolution set as a range in a form of start-end:step, where step is an optional parameter and is equal to 0.1 by default.
3. Updated UCSC Cellbrowser to 1.2.8.
4. Save gene and peak markers in the same rds file as the main Seurat object.
5. Export multiple resolutions with the correspondent gene and peaks markers into the UCSC Cellbrowser.
6. Fixed a bug in the heatmaps when exporting gene markers from the multiple resolutions.
7. Added NA color for not assigned cell cycle phase, otherwise fails to output some of the plots.
8. Added "Single-Cell RNA-Seq Reference Mapping" (sc-rna-azimuth.cwl) pipeline. Tags: Single-Cell, Seurat, Azimuth, Cell-Type-Assignment, Rerefence-Based-Mapping.
9. Added "Single-cell RNA-Seq BD Rhapsody Import" (sc-rna-load-rhapsody.cwl) pipeline. Tags: Single-Cell, Seurat, BD-Rhapsody, Utilities.
10. Export Azimuth reference model from the sc-ctype-assign.cwl pipeline
11. Replaces cumulusprod/cellranger-arc:2.0.2 with biowardrobe2/cellranger-arc:v0.0.1 because otherwise
    it fails on this check if not os.access(output_parent_dir, os.W_OK) when running on NFS storage even if we have all required permissions.
12. Updated sc-ctype-assign.cwl, sc-rna-azimuth.cwl, sc-rna-cluster.cwl, and sc-wnn-cluster.cwl pipelines with genesets_data input to calculate module scores for each gene set.
13. Updated soon be deprecated pipeline deseq-multi-factor.cwl to use biowardrobe2/deseq:v0.0.7 docker image that doesn't fail with those auto estimated contrasts which don't have enough replicates.
14. Updated sc-rna-da-cells.cwl workflow to support RNA, ATAC, and WNN clustering as inputs. Fixed Bugs.
15. Updated sc-ctype-assign.cwl workflow to allow filtering by the user provided barcodes.
16. Updated trim-atacseq-pe.cwl, trim-atacseq-se.cwl, trim-chipseq-pe.cwl, trim-chipseq-se.cwl, trim-rnaseq-pe-dutp.cwl, trim-rnaseq-pe.cwl, trim-rnaseq-se-dutp.cwl, and trim-rnaseq-se.cwl pipelines with the optional input to provide the minimum length to discard reads after adapter trimming.

Before merging, make sure that the following bugs have been fixed:

• Heatmap shows wrong clusters when multiple resolutions are used in the RNA/WNN clustering pipelines.
• Sometimes cell cycle scores are NA, that breaks certain plots
• When Peak markers enabled, UCSC Cell Browser fails to export ATAC assay
• Select proper tags for the "Single-Cell RNA-Seq Reference Mapping" pipeline
• Select proper tags for the "Single-cell RNA-Seq BD Rhapsody Import" pipeline
• Make sure we use a docker image for a fastq-dump tool that have --max-size set to a big value
• Subsetting RNA reduction by barcodes makes WNN clustering mix the cells, because it changes the cells order only in one of the assays.
• DA pipeline has wrong color scale on the UMAP (should have three colors, not two)
• DA pipeline doesn't export UCSC Cell Browser
• Test if it's a bug and fix it - can't run RNA clustering after ATAC reduction. FindNeighbors doesn't return the required graph.