Currently, show-params prints a placeholder html link to a tool in the workflow like this:
snakemake-run-cellranger show-params --step demultiplexing --method demuxalot
============================================================
Parameters for: demultiplexing.demuxalot
Tool: demuxalot v0.4.3
URL: https://github.com/arogozhnikov/demuxalot
============================================================
vcf
Type: string
Status: REQUIRED
Description: Path to VCF file with genotypes
genome_names
Type: string
Status: REQUIRED
Description: Path to txt file with genome names
refine
Type: boolean
Status: REQUIRED
Description: Run genotype refinement step. Read more here: https://github.com/arogozhnikov/demuxalot?tab=readme-ov-file#running-complex-scenario
celltag
Type: string
Status: optional (default: CB)
Description: Cell barcode tag in BAM file
umitag
Type: string
Status: optional (default: UB)
Description: UMI tag in BAM fileWhat would be BETTER is if it linked to a stable release of the tool so the external documentations lines up exactly with the our release and users don't get confused about what params are available to them.
Currently,
show-paramsprints a placeholder html link to a tool in the workflow like this:snakemake-run-cellranger show-params --step demultiplexing --method demuxalot ============================================================ Parameters for: demultiplexing.demuxalot Tool: demuxalot v0.4.3 URL: https://github.com/arogozhnikov/demuxalot ============================================================ vcf Type: string Status: REQUIRED Description: Path to VCF file with genotypes genome_names Type: string Status: REQUIRED Description: Path to txt file with genome names refine Type: boolean Status: REQUIRED Description: Run genotype refinement step. Read more here: https://github.com/arogozhnikov/demuxalot?tab=readme-ov-file#running-complex-scenario celltag Type: string Status: optional (default: CB) Description: Cell barcode tag in BAM file umitag Type: string Status: optional (default: UB) Description: UMI tag in BAM fileWhat would be BETTER is if it linked to a stable release of the tool so the external documentations lines up exactly with the our release and users don't get confused about what params are available to them.