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Amrfinderplus: add db-version to versions.yml (#1899)

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* not yet working: add db version to versions.yml

* next try: db version number not in versions.yml

* Fix amrfinderplus versioning

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Dump version for syncrony with run

* Update test.yml

* Apply suggestions from code review

Co-authored-by: James Fellows Yates <jfy133@gmail.com>
This commit is contained in:
louperelo 2022-07-19 09:52:36 +02:00 committed by GitHub
parent 035e418369
commit 8002e373b5
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
4 changed files with 9 additions and 13 deletions
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7
modules/amrfinderplus/run/main.nf
View file

@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null) conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : 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/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
@ -50,6 +50,7 @@ process AMRFINDERPLUS_RUN {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
amrfinderplus: \$(amrfinder --version) amrfinderplus: \$(amrfinder --version)
amrfinderplus-database: \$(echo \$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev))
END_VERSIONS END_VERSIONS
""" """
} }

6
modules/amrfinderplus/update/main.nf
View file

@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE {
tag "update" tag "update"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null) conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : 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/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
output: output:
path "amrfinderdb.tar.gz", emit: db path "amrfinderdb.tar.gz", emit: db

7
tests/modules/amrfinderplus/run/test.yml
View file

@ -1,11 +1,8 @@
- name: amrfinderplus run test_amrfinderplus_run - name: amrfinderplus run test_amrfinderplus_run
command: nextflow run tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c tests/config/nextflow.config command: nextflow run ./tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config -c ./tests/modules/amrfinderplus/run/nextflow.config
tags: tags:
- amrfinderplus/run
- amrfinderplus - amrfinderplus
- amrfinderplus/run
files: files:
- path: output/amrfinderplus/amrfinderdb.tar.gz
- path: output/amrfinderplus/test.tsv - path: output/amrfinderplus/test.tsv
md5sum: b4d261ace9be7d013c19d1f5c0005bfe md5sum: b4d261ace9be7d013c19d1f5c0005bfe
- path: output/amrfinderplus/versions.yml
md5sum: 642ca04a07d79fe4c4d02348562e3961

2
tests/modules/amrfinderplus/update/test.yml
View file

@ -5,5 +5,3 @@
- amrfinderplus/update - amrfinderplus/update
files: files:
- path: output/amrfinderplus/amrfinderdb.tar.gz - path: output/amrfinderplus/amrfinderdb.tar.gz
- path: output/amrfinderplus/versions.yml
md5sum: 4db18fa509309db4da0920a7eeaba86c