nf-core_modules/tests/software/last/postmask/test.yml at ca321ce69d3cf167e8057c0d6fc075b089a769c5 - millironx/nf-core_modules - Milliron X Code: Code hosting for cattle or technology, but especially anything to do with both of them

millironx/nf-core_modules

mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-22 08:12:03 +00:00

Charles Plessy ca321ce69d

New module last/postmask to filter alignment files (#526 )

The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.

As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline.  I added a check
that gives a clearer error message in this case.  Please let me know
what you think about; I can add this test to the existing LAST modules
as well.

This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.

2021-06-08 11:14:08 +02:00

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 - name: last postmask test_last_postmask
   command: nextflow run tests/software/last/postmask -entry test_last_postmask -c tests/config/nextflow.config
   tags:
     - last
     - last/postmask
   files:
     - path: output/last/contigs.genome.postmask.maf.gz
       md5sum: 3a0f42e76da9549748983ac4d7ff7473