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nf-core / bamtofastq

Converts bam or cram files to fastq format and does quality control.
https://nf-co.re/bamtofastq
MIT License
16 stars 13 forks source link

Important! Template update for nf-core/tools v2.14.0 #89

Closed nf-core-bot closed 3 months ago

nf-core-bot commented 3 months ago

Version 2.14.0 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.14.0 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.14.0 release page.

asp8200 commented 3 months ago

@maxulysse : Should we try and get this merged?

mirpedrol commented 3 months ago

It seems that the PR is running the initialisation of that fasta param to null - why is that?

Some versions ago when we introduced the nf-validation plugin we change the order in which we retrieve genomes. Due to this change, having fasta = null prevents the function to retrieve a fast file from igenomes when using --genome. The solution is to remove the initialisation of the fasta param from nextflow.config.

Note that you will need to add the parameter to validationSchemaIgnoreParams, to avoid nf-validation warnings.

nf-core-bot commented 3 months ago

Version 2.14.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of https://github.com/nf-core/bamtofastq/pull/91

Please use https://github.com/nf-core/bamtofastq/pull/91 to merge in the new changes from the nf-core template as soon as possible.