diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml index 50649124cc81..7a297b1c0bb7 100644 --- a/.github/actions/nf-test-action/action.yml +++ b/.github/actions/nf-test-action/action.yml @@ -58,7 +58,7 @@ runs: if: ${{contains(inputs.profile, 'conda')}} uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 with: - auto-update-conda: true + miniconda-version: "py312_24.11.1-0" conda-solver: libmamba conda-remove-defaults: true diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index add68966cf3b..3e47ed1a3fb9 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -4,8 +4,8 @@ process PHYLOFLASH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/phyloflash:3.4.2--hdfd78af_1' : - 'quay.io/biocontainers/phyloflash:3.4.2--hdfd78af_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d993344c3f636cb0cca9519b11fcf30faafb13fca2fd33090104e5f52d8fd643/data' : + 'community.wave.seqera.io/library/phyloflash:3.4.2--87628969a9477d43' }" input: tuple val(meta), path(reads) @@ -14,7 +14,7 @@ process PHYLOFLASH { output: tuple val(meta), path("${meta.id}*/*"), emit: results - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('phyloflash'), eval("phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//'"), topic: versions, emit: versions_phyloflash when: task.ext.when == null || task.ext.when @@ -25,38 +25,28 @@ process PHYLOFLASH { if (meta.single_end) { """ phyloFlash.pl \\ - $args \\ + ${args} \\ -read1 ${reads[0]} \\ - -lib $prefix \\ + -lib ${prefix} \\ -interleaved \\ -dbhome . \\ - -CPUs $task.cpus + -CPUs ${task.cpus} - mkdir $prefix - mv ${prefix}.* $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//") - END_VERSIONS + mkdir ${prefix} + mv ${prefix}.* ${prefix} """ } else { """ phyloFlash.pl \\ - $args \\ + ${args} \\ -read1 ${reads[0]} \\ -read2 ${reads[1]} \\ - -lib $prefix \\ + -lib ${prefix} \\ -dbhome . \\ - -CPUs $task.cpus - - mkdir $prefix - mv ${prefix}.* $prefix + -CPUs ${task.cpus} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//") - END_VERSIONS + mkdir ${prefix} + mv ${prefix}.* ${prefix} """ } @@ -66,10 +56,5 @@ process PHYLOFLASH { mkdir ${prefix} touch ${prefix}/${prefix}.SSU.collection.fasta touch ${prefix}/${prefix}.phyloFlash - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//") - END_VERSIONS """ } diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index 46b4cb106374..0a3d370ef383 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -1,19 +1,18 @@ name: phyloflash -description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore - phylogenetic composition of an illumina (meta)genomic dataset. +description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. keywords: - metagenomics - illumina datasets - phylogenetic composition tools: - phyloflash: - description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and - explore phylogenetic composition of an illumina (meta)genomic dataset. + description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. homepage: https://hrgv.github.io/phyloFlash/ documentation: https://hrgv.github.io/phyloFlash/usage.html tool_dev_url: https://github.com/HRGV/phyloFlash doi: "10.1128/mSystems.00920-20" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:phyloflash input: - - meta: @@ -44,13 +43,29 @@ output: type: directory description: Folder containing the results of phyloFlash analysis pattern: "${prefix}*" + versions_phyloflash: + - - ${task.process}: + type: string + description: The name of the process + - phyloflash: + type: string + description: The name of the tool + - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//': + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - phyloflash: + type: string + description: The name of the tool + - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//': + type: eval + description: The expression to obtain the version of the tool + authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/phyloflash/tests/main.nf.test b/modules/nf-core/phyloflash/tests/main.nf.test index 4434aa3ffdc4..0fd5b120fe76 100644 --- a/modules/nf-core/phyloflash/tests/main.nf.test +++ b/modules/nf-core/phyloflash/tests/main.nf.test @@ -30,10 +30,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot( - process.out, - path(process.out.versions[0]).yaml - ).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/phyloflash/tests/main.nf.test.snap b/modules/nf-core/phyloflash/tests/main.nf.test.snap index f38feaee041c..81979b3a1802 100644 --- a/modules/nf-core/phyloflash/tests/main.nf.test.snap +++ b/modules/nf-core/phyloflash/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "test_phyloflash_single_end -- stub": { "content": [ { - "0": [ + "results": [ [ { "id": "test", @@ -14,35 +14,19 @@ ] ] ], - "1": [ - "versions.yml:md5,4880b2dc7060ad23366127e99619a2af" - ], - "results": [ + "versions_phyloflash": [ [ - { - "id": "test", - "single_end": true - }, - [ - "test.SSU.collection.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.phyloFlash:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "PHYLOFLASH", + "phyloflash", + "3.4.2" ] - ], - "versions": [ - "versions.yml:md5,4880b2dc7060ad23366127e99619a2af" ] - }, - { - "PHYLOFLASH": { - "phyloflash": "3.4.2" - } } ], + "timestamp": "2026-08-04T16:21:31.167874643", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" - }, - "timestamp": "2025-05-14T12:18:39.919595406" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file