diff --git a/modules/amrfinderplus/run/main.nf b/modules/amrfinderplus/run/main.nf index 47a8fb46..d60c3da4 100644 --- a/modules/amrfinderplus/run/main.nf +++ b/modules/amrfinderplus/run/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null) + conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': - 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': + 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }" input: tuple val(meta), path(fasta) @@ -50,6 +50,7 @@ process AMRFINDERPLUS_RUN { cat <<-END_VERSIONS > versions.yml "${task.process}": amrfinderplus: \$(amrfinder --version) + amrfinderplus-database: \$(echo \$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)) END_VERSIONS """ } diff --git a/modules/amrfinderplus/update/main.nf b/modules/amrfinderplus/update/main.nf index ad09c391..811c2522 100644 --- a/modules/amrfinderplus/update/main.nf +++ b/modules/amrfinderplus/update/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE { tag "update" label 'process_low' - conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null) + conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': - 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': + 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }" output: path "amrfinderdb.tar.gz", emit: db diff --git a/tests/modules/amrfinderplus/run/test.yml b/tests/modules/amrfinderplus/run/test.yml index d858cb88..0529fe13 100644 --- a/tests/modules/amrfinderplus/run/test.yml +++ b/tests/modules/amrfinderplus/run/test.yml @@ -1,11 +1,8 @@ - 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: - - amrfinderplus/run - amrfinderplus + - amrfinderplus/run files: - - path: output/amrfinderplus/amrfinderdb.tar.gz - path: output/amrfinderplus/test.tsv md5sum: b4d261ace9be7d013c19d1f5c0005bfe - - path: output/amrfinderplus/versions.yml - md5sum: 642ca04a07d79fe4c4d02348562e3961 diff --git a/tests/modules/amrfinderplus/update/test.yml b/tests/modules/amrfinderplus/update/test.yml index 7ae89992..df26973b 100644 --- a/tests/modules/amrfinderplus/update/test.yml +++ b/tests/modules/amrfinderplus/update/test.yml @@ -5,5 +5,3 @@ - amrfinderplus/update files: - path: output/amrfinderplus/amrfinderdb.tar.gz - - path: output/amrfinderplus/versions.yml - md5sum: 4db18fa509309db4da0920a7eeaba86c