Not able to run nallo without --vep_cache

[lasseringstedmark]

Description of the bug

It does not seems to be possible to run Nallo version 0.4.0 without specifing --vep_cache even with --skip_snv_annotation

The following error are present

WARN: Access to undefined parameter `genomes` -- Initialise it to a default value eg. `params.genomes = some_value`
[-        ] process > GENOMICMEDICINESWEDEN_NALLO:NALLO:CONVERT_INPUT_FILES:SAMTOOLS_FASTQ  -
[-        ] process > GENOMICMEDICINESWEDEN_NALLO:NALLO:CONVERT_INPUT_FILES:SAMTOOLS_IMPORT -
ERROR ~ Cannot invoke method endsWith() on null object

 -- Check script '.nextflow/assets/genomic-medicine-sweden/nallo/./workflows/nallo.nf' at line: 131 or see '.nextflow.log' file for more details

From the file nallo.nf specified in above

    126         // Prepeare references
    127         PREPARE_GENOME (
    128             ch_fasta,
    129             ch_vep_cache_unprocessed,
    130             params.fasta.endsWith('.gz'),       // should we unzip fasta
    131             params.vep_cache.endsWith("tar.gz") // should we untar vep cache
    132         )
    133         ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
    134

When looking into the nallo.nf from former version 0.3.2, there are some checks on params.vep_cache, which seems to be missing in version 0.4.0

    //
    // Prepare references
    //
    if(!params.skip_mapping_wf | !params.skip_assembly_wf ) {

        PREPARE_GENOME (
            ch_fasta,
            ch_vep_cache_unprocessed,
        )
        ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)

        if(!params.skip_snv_annotation) {
            if (params.vep_cache) {
                if (params.vep_cache.endsWith("tar.gz")) {
                    ch_vep_cache = PREPARE_GENOME.out.vep_resources
                } else {
                    ch_vep_cache = Channel.fromPath(params.vep_cache).collect()
                }
            }
        }

When I specify --vep_cache it works fine. Both with and without --skip_snv_annotation

The documentation does not say anything vep_cache being mandatory. Is this as intended or a bug?

Settings
Nextflow version 24.04.2
Nallo version 0.4.0
Running with Docker

Command used and terminal output

Relevant files

No response

System information

No response

[fellen31]

Hi, thanks for reporting this.

It's indeed a bug, the CI-tests always run without any of the --skip´s so this has slipped through (hope to adress this soon). Also, I see the I have missed a point in the documentation.

The pipeline should be able to run without --vep_cache if you also have both of these active:

• --skip_snv_annotation (--vep_cache is mandatory for SNV annotation, this is stated in the documentation: https://genomic-medicine-sweden.github.io/nallo/0.4.0/usage/#snv-annotation) and
• --skip_sv_annotation (this is missing from the documentation).

Will try to get a fix out for this soon.

[lasseringstedmark]

@fellen31 sounds good!

Just to let you know - I did actually run with both parameters --skip_snv_annotation and --skip_sv_annotation, so I think this behaviour are present regardsless of this.

[fellen31]

@fellen31 sounds good!

Just to let you know - I did actually run with both parameters --skip_snv_annotation and --skip_sv_annotation, so I think this behaviour are present regardsless of this.

You are right, I meant should in the sense that's how I'd like it to work, but currently it does not 😅

[fellen31]

Hi, sorry for the delay. I have a patch that I think should solve this (#553).

Would you be able to try running the pipeline with the patch branch (nextflow run genomic-medicine-sweden/nallo -r patch) to ensure that it fixes your issue?

[fellen31]

Released as 0.4.1.

Let me know if you have any more issues!