Include local modules into nf-core - Githubissues

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

GNU General Public License v3.0

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Include local modules into nf-core #96

Open mahesh-panchal opened 1 year ago

mahesh-panchal commented 1 year ago

We have a lot of modules that are not managed by nf-core. It would be nice to have them managed by nf-core.

modules/local/agat/extractsequences.nf
modules/local/agat/filterbyattribute.nf
modules/local/agat/filterbylocusdistance.nf
modules/local/agat/filterbymrnablastvalue.nf
modules/local/agat/filterincompletegenecodingmodels.nf
modules/local/agat/gff2zff.nf
modules/local/agat/keeplongestisoform.nf
modules/local/agat/managefunctionalannotation.nf
modules/local/agat/separatebyrecord.nf
modules/local/augustus/gbk2augustus.nf
modules/local/augustus/gff2gbk.nf
modules/local/augustus/training.nf
modules/local/blast/blastp.nf
modules/local/gaas/fastapurify.nf
modules/local/gaas/fastastatistics.nf
modules/local/snap/training.nf
modules/local/stringtie/stringtie.nf

These use a combined container, and might require special treatment.

modules/local/hisat2/align.nf
modules/local/hisat2/build.nf

The tool in this module does not behave well. This may be very involved:

modules/local/interproscan.nf

Note: Individual bullet points can be converted into issues to have single issues for specific modules being worked on.

mahesh-panchal commented 1 year ago

Nf-core module for interproscan exists: https://github.com/nf-core/modules/blob/master/modules/nf-core/interproscan/main.nf