Leon Rauschning

Update learnmsa module to work with compressed files.

1

Add the compression handling introduced to MSA modules in #4754 to learnmsa (forgot learnmsa and kalign it in that PR).

Add the compression handling introduced to MSA modules in https://github.com/nf-core/modules/pull/4754 to kalign (forgot learnmsa and kalign it in that PR).

Was thinking on adding support for handling xz-compressed files, as we do right now with gzip, to nf-test. Had this idea while looking at nf-core/modules#526, and started coding something up...

Mismatch by one space just caught my eye.

sort hash.tsv

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Sorts hash.tsv lexically. LMK if this is desirable.

Add option to pass additional parameters when submitting jobs to the grid

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Hi, our local slurm cluster is configured in such a way that additional parameters are required when submitting jobs, and the job ID may contain a semicolon. This commit enables...

Came across an issue with how some bash shells handle anonymous named pipes that causes tcoffee to interpret it as a parameter and fail. This commit should make it a...

add UPP

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Adds a module for running MSA using UPP to nf-core. As there are some issues with the conda package for SEPP/UPP, this is drafted for now. - [X] This comment...

Hi Heng, as discussed at IGGSy, this PR exposes the `sc_ambi` and `max_gaplen` parameters already exposed on the CLI interface in the cython/mappy interface as well. Same as other options...