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update bakta to latest version (v1.4.0) (#1428)

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* update bakta to latest version (v1.4.0)

* Update test.yml

* remove empty file md5sums

* bakta was rebuilt to fix dependencies on bioconda

* trigger ci

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
This commit is contained in:
Robert A. Petit III 2022-03-24 10:49:17 -06:00 committed by GitHub
parent debbcd98eb
commit dfbb0bc17c
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3 changed files with 4 additions and 15 deletions
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6
modules/bakta/main.nf
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@ -2,10 +2,10 @@ process BAKTA {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::bakta=1.3.1" : null) conda (params.enable_conda ? "bioconda::bakta=1.4.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' : 'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }" 'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

2
modules/bakta/meta.yml
View file

@ -78,7 +78,7 @@ output:
pattern: "*.ffn" pattern: "*.ffn"
- hypotheticals_tsv: - hypotheticals_tsv:
type: file type: file
description: further information on hypothetical protein CDS as simple human readble tab separated values description: additional information on hypothetical protein CDS as simple human readble tab separated values
pattern: "*.hypotheticals.tsv" pattern: "*.hypotheticals.tsv"
- hypotheticals_faa: - hypotheticals_faa:
type: file type: file

11
tests/modules/bakta/test.yml
View file

@ -1,25 +1,14 @@
## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml bakta
- name: bakta - name: bakta
command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run
tags: tags:
- bakta - bakta
files: files:
- path: output/bakta/test.embl - path: output/bakta/test.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.faa - path: output/bakta/test.faa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.ffn - path: output/bakta/test.ffn
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.fna - path: output/bakta/test.fna
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.gbff - path: output/bakta/test.gbff
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.gff3 - path: output/bakta/test.gff3
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.hypotheticals.tsv - path: output/bakta/test.hypotheticals.tsv
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.hypotheticals.faa - path: output/bakta/test.hypotheticals.faa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.tsv - path: output/bakta/test.tsv
md5sum: d41d8cd98f00b204e9800998ecf8427e