updating modules, adding defaults and making mandatory arguments mandatory#87
updating modules, adding defaults and making mandatory arguments mandatory#87ferenckata wants to merge 12 commits intodevfrom
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… nf-test-and-fix-dev
…ow the update broke it back to original
| output: | ||
| path "BSgenome.*.tar.gz", emit: bsgenome | ||
| path "versions.yml", emit: versions | ||
| path "versions.yml", emit: versions, topic: versions |
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that's not how the new version topics work, you don't emit the yml file, but the version parsing itself, see https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules
instead of copying it to local I would either install the specific older version or make a module patch https://nf-co.re/docs/nf-core-tools/modules/patch so you can still benefit from the upstream changes (and also makes reviewing the pipeline easier) |
Note: one issue remains with the inclusion of pipeline info into multiqc, which I asked about at nf-core slack.
Below is a set of arguments that runs the code. The highlighted ones are mandatory (bsgenome is mandatory if no forging)
nextflow run cageseq/main.nf --infolder cageflow_test_data/fastq/pe --gtf cageflow_test_data/danRer11_genome/danRer11.ensGene.gtf --outdir testout --genome cageflow_test_data/danRer11_genome/danRer11.fa --bsgenome BSgenome.Drerio.UCSC.danRer11 -profile singularity --seq_platform test --sample_name_fields 1 --index cageflow_test_data/danRer11_genome/star
The issue with ucsc wig to bigwig conversion was that it was changed ~2 years ago to support paired-end reads, but since it was not moved to local, it got updated back to the original version now (i.e., not supporting paired-end reads anymore, which is the default behaviour). I reverted the changes and moved it to local.