Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true

[RHReynolds]

Description of the bug

If the pipeline is run with the test profile, with no transcript fasta provided and --skip_gtf_filter enabled, it fails due to the following error:

Access to 'GTF_FILTER.out' is undefined since the process 'GTF_FILTER' has not been invoked before accessing the output attribute

 -- Check script '/Users/rreynolds/pipeline_development/nf-core-rnaseq/./workflows/../subworkflows/local/prepare_genome/main.nf' at line: 149 or see '.nextflow.log' file for more details

This appears to be due to the following line, in the PREPARE_GENOME module:

ch_versions         = ch_versions.mix(GTF_FILTER.out.versions)

The GTF_FILTER versions is already defined in line 97 of the same script, so I'm not sure it's required again here. Removing this line also appears to resolve the issue. Going to put in a PR with this change.

Command used and terminal output

nextflow run ../nf-core-rnaseq -profile test,docker,arm --skip_gtf_filter --outdir rnaseq-test-skip --aligner star_salmon

Relevant files

Nextflow log: nextflow.log
Modified test config, with transcript_fasta commented out:

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a fast and simple pipeline test.

    Use as follows:
        nextflow run nf-core/rnaseq -profile test,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
    config_profile_name        = 'Test profile'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Limit resources so that this can run on GitHub Actions
    max_cpus   = 2
    max_memory = '6.GB'
    max_time   = '6.h'


    // Input data
    input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv"

    // Genome references
    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"
    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz"
    // transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta"
    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz"

    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt"
    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz"
    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz"
    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz"

    // Other parameters
    skip_bbsplit        = false
    pseudo_aligner      = 'salmon'
    umitools_bc_pattern = 'NNNN'
}

// When using RSEM, remove warning from STAR whilst building tiny indices
process {
    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
        ext.args2 = "--genomeSAindexNbases 7"
    }
}

System information

• Nextflow version: 23.04.1
• Hardware: Desktop
• Executor: local
• Container engine: Docker
• OS: macOS
• Version of nf-core/rnaseq: 3.13.1

[pinin4fjords]

fixed in #1126