--cellranger_index only appears to work if --validate_params false provided

[nick-youngblut]

Description of the bug

The CellRanger index is a directory of files, and not just one. So, one should provide a directory via --cellranger_index; however, this throws the following error:

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --cellranger_index: '/large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/' is not a file, but a directory (/large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/)

It appears that the parameter validation is checking that the --cellranger_index is a file and not a directory. If I skip the validation via --validate_params false, then the pipeline will complete the CellRanger Count step.

Command used and terminal output

nextflow run main.nf \
   -profile test_full,singularity \
   -process.executor slurm \
   -process.queue cpu_batch \
   --aligner cellranger \
   --cellranger_index /large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/ \
   --outdir test_run_output \
   --validate_params false

Relevant files

No response

System information

Nextflow version: 23.10.1.5891
Hardware: HPC
Executor: SLURM
Container engine: Apptainer
OS: Ubuntu
Version of nf-core/scrnaseq: 2.6.0

[nick-youngblut]

Along these same lines:

In subworkflows/local/align_cellranger.nf, the code is:

        assert cellranger_index || (fasta && gtf):
            "Must provide either a cellranger index or both a fasta file ('--fasta') and a gtf file ('--gtf')."

        if (!cellranger_index) {
            // Filter GTF based on gene biotypes passed in params.modules
            CELLRANGER_MKGTF( gtf )
            ch_versions = ch_versions.mix(CELLRANGER_MKGTF.out.versions)

            // Make reference genome
            CELLRANGER_MKREF( fasta, CELLRANGER_MKGTF.out.gtf, "cellranger_reference" )
            ch_versions = ch_versions.mix(CELLRANGER_MKREF.out.versions)
            cellranger_index = CELLRANGER_MKREF.out.reference
        }

...so based on "Must provide either a cellranger index or both a fasta file ('--fasta') and a gtf file ('--gtf').", one can assume that if --cellranger_index is provided, then --gtf and --fasta do not need to be provided.

However, if one does not not provide --gtf and --fasta, then warnings are generated:

WARN: Access to undefined parameter `gtf` -- Initialise it to a default value eg. `params.gtf = some_value`
WARN: Access to undefined parameter `fasta` -- Initialise it to a default value eg. `params.fasta = some_value`

These warnings seem to be an unnecessary distraction (possibly leading to confusion), if the user provides --cellranger_index instead of --gtf and --fasta.

[grst]

First problem should already be fixed in v2.7.
Second problem will be fixed in #354.

[grst]

Fixed in dev