From fc2a5c4f9f4b88929ef84cff7218f7a6485c89b3 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Fri, 1 May 2026 16:17:58 +0100 Subject: [PATCH 1/5] nf-core-module-dev bots updating hmmer tools: hmmbuild, hmmsearch, hmmalign to topic versions and latest standards --- modules/nf-core/hmmer/hmmalign/main.nf | 14 +- modules/nf-core/hmmer/hmmalign/meta.yml | 28 +++- .../nf-core/hmmer/hmmalign/tests/main.nf.test | 4 +- .../hmmer/hmmalign/tests/main.nf.test.snap | 50 +++---- modules/nf-core/hmmer/hmmbuild/main.nf | 14 +- modules/nf-core/hmmer/hmmbuild/meta.yml | 36 +++-- .../nf-core/hmmer/hmmbuild/tests/main.nf.test | 13 +- .../hmmer/hmmbuild/tests/main.nf.test.snap | 59 ++++---- modules/nf-core/hmmer/hmmsearch/main.nf | 15 +- modules/nf-core/hmmer/hmmsearch/meta.yml | 28 +++- .../hmmer/hmmsearch/tests/main.nf.test | 16 +- .../hmmer/hmmsearch/tests/main.nf.test.snap | 138 +++++++----------- 12 files changed, 196 insertions(+), 219 deletions(-) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index d51a94f80290..1f9edaa30e2f 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -13,7 +13,7 @@ process HMMER_HMMALIGN { output: tuple val(meta), path("*.sto.gz"), emit: sto - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("hmmer"), eval("hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer when: task.ext.when == null || task.ext.when @@ -26,21 +26,11 @@ process HMMER_HMMALIGN { $args \\ $hmm \\ $fasta | gzip -c > ${prefix}.sto.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - echo | gzip > ${prefix}.sto.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') - END_VERSIONS + echo "" | gzip > ${prefix}.sto.gz """ } diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml index c5d7b2cc7f78..6f095a04a0ec 100644 --- a/modules/nf-core/hmmer/hmmalign/meta.yml +++ b/modules/nf-core/hmmer/hmmalign/meta.yml @@ -45,13 +45,29 @@ output: pattern: "*.sto.gz" ontologies: - edam: http://edamontology.org/format_3989 # GZIP format + versions_hmmer: + - - ${task.process}: + type: string + description: The process name + - hmmer: + type: string + description: The tool name + - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + +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 process name + - hmmer: + type: string + description: The tool name + - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + authors: - "@erikrikarddaniel" - "@jfy133" diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test index 7b0368fc630d..59f2d8709641 100644 --- a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -50,7 +50,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap index ae65cacb18b2..d06dd208c137 100644 --- a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap +++ b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "test-hmmer-hmmalign": { "content": [ { - "0": [ + "sto": [ [ { "id": "test" @@ -10,32 +10,25 @@ "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f" ] ], - "1": [ - "versions.yml:md5,601e13e7a1e6057766d862a828d501c4" - ], - "sto": [ + "versions_hmmer": [ [ - { - "id": "test" - }, - "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f" + "HMMER_HMMALIGN", + "hmmer", + "3.4" ] - ], - "versions": [ - "versions.yml:md5,601e13e7a1e6057766d862a828d501c4" ] } ], + "timestamp": "2026-05-01T15:54:13.981909183", "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - }, - "timestamp": "2024-11-13T12:37:26.551497424" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "test-hmmer-hmmalign-stub": { "content": [ { - "0": [ + "sto": [ [ { "id": "test" @@ -43,26 +36,19 @@ "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "1": [ - "versions.yml:md5,601e13e7a1e6057766d862a828d501c4" - ], - "sto": [ + "versions_hmmer": [ [ - { - "id": "test" - }, - "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "HMMER_HMMALIGN", + "hmmer", + "3.4" ] - ], - "versions": [ - "versions.yml:md5,601e13e7a1e6057766d862a828d501c4" ] } ], + "timestamp": "2026-05-01T15:54:21.354318795", "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - }, - "timestamp": "2024-11-13T12:37:32.244343836" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 7a61bd0440fd..1b5b263102f5 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -14,7 +14,7 @@ process HMMER_HMMBUILD { output: tuple val(meta), path("*.hmm.gz"), emit: hmm path "*.hmmbuild.txt", emit: hmmbuildout - path "versions.yml", emit: versions + tuple val("${task.process}"), val("hmmer"), eval("hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer when: task.ext.when == null || task.ext.when @@ -35,22 +35,12 @@ process HMMER_HMMBUILD { $alignment gzip ${prefix}.hmm - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - echo | gzip > ${prefix}.hmm.gz + echo "" | gzip > ${prefix}.hmm.gz touch ${prefix}.hmmbuild.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) - END_VERSIONS """ } diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index db474a394c45..be03297974d9 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -36,10 +36,10 @@ input: output: hmm: - - meta: - type: file - description: Gzipped HMM file - pattern: "*.{hmm.gz}" - ontologies: [] + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*.hmm.gz": type: file description: Gzipped HMM file @@ -50,13 +50,29 @@ output: type: file description: HMM build output ontologies: [] + versions_hmmer: + - - ${task.process}: + type: string + description: The process name + - hmmer: + type: string + description: The tool name + - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + +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 process name + - hmmer: + type: string + description: The tool name + - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test index 635f5b661f15..9367870639a7 100644 --- a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_process { [ id: 'PF14720' ], // meta map file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) ] - input[1] = [] + input[1] = [] """ } @@ -29,12 +29,7 @@ nextflow_process { assertAll( { assert process.success }, { assert file(process.out.hmmbuildout[0]).text.contains('CPU time:') }, - { assert snapshot( - file(process.out.hmm[0][1]).name, // unstable - file(process.out.hmmbuildout[0]).name, // unstable - process.out.versions - ).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["hmm", "hmmbuildout"])).match() } ) } } @@ -49,7 +44,7 @@ nextflow_process { [ id: 'PF14720' ], // meta map file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) ] - input[1] = [] + input[1] = [] """ } @@ -58,7 +53,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap index 79317b89ebd1..e91af9e4fb65 100644 --- a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "test-hmmer-hmmbuild-stub": { "content": [ { - "0": [ + "hmm": [ [ { "id": "PF14720" @@ -10,46 +10,51 @@ "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "1": [ + "hmmbuildout": [ "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], - "2": [ - "versions.yml:md5,f8a0bffcbbc58404752849403812905b" - ], + "versions_hmmer": [ + [ + "HMMER_HMMBUILD", + "hmmer", + "3.4" + ] + ] + } + ], + "timestamp": "2026-05-01T16:02:22.362282382", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "test-hmmer-hmmbuild": { + "content": [ + { "hmm": [ [ { "id": "PF14720" }, - "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "PF14720.hmm.gz" ] ], "hmmbuildout": [ - "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "PF14720.hmmbuild.txt" ], - "versions": [ - "versions.yml:md5,f8a0bffcbbc58404752849403812905b" + "versions_hmmer": [ + [ + "HMMER_HMMBUILD", + "hmmer", + "3.4" + ] ] } ], + "timestamp": "2026-05-01T16:02:17.152231892", "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - }, - "timestamp": "2024-11-13T12:52:29.794123574" - }, - "test-hmmer-hmmbuild": { - "content": [ - "PF14720.hmm.gz", - "PF14720.hmmbuild.txt", - [ - "versions.yml:md5,f8a0bffcbbc58404752849403812905b" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - }, - "timestamp": "2024-11-13T12:52:23.95935055" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index de5fd150ef8c..7d823b1f4141 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -4,8 +4,8 @@ process HMMER_HMMSEARCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmmer:3.4--hdbdd923_1' : - 'quay.io/biocontainers/hmmer:3.4--hdbdd923_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' : + 'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }" input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) @@ -15,7 +15,7 @@ process HMMER_HMMSEARCH { tuple val(meta), path('*.sto.gz') , emit: alignments , optional: true tuple val(meta), path('*.tbl.gz') , emit: target_summary, optional: true tuple val(meta), path('*.domtbl.gz'), emit: domain_summary, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("hmmer"), eval("hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer when: task.ext.when == null || task.ext.when @@ -43,10 +43,6 @@ process HMMER_HMMSEARCH { ${write_target ? '*.tbl' : ''} \\ ${write_domain ? '*.domtbl' : ''} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') - END_VERSIONS """ stub: @@ -61,10 +57,5 @@ process HMMER_HMMSEARCH { ${write_align ? '*.sto' : ''} \\ ${write_target ? '*.tbl' : ''} \\ ${write_domain ? '*.domtbl' : ''} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmmer: \$(hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') - END_VERSIONS """ } diff --git a/modules/nf-core/hmmer/hmmsearch/meta.yml b/modules/nf-core/hmmer/hmmsearch/meta.yml index 97daa54790e9..62d3f9e712ae 100644 --- a/modules/nf-core/hmmer/hmmsearch/meta.yml +++ b/modules/nf-core/hmmer/hmmsearch/meta.yml @@ -87,13 +87,29 @@ output: description: Optional tabular (space-delimited) summary of per-domain output pattern: "*.{domtbl.gz}" ontologies: [] + versions_hmmer: + - - ${task.process}: + type: string + description: The process name + - hmmer: + type: string + description: The tool name + - hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + +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 process name + - hmmer: + type: string + description: The tool name + - hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + type: eval + description: The tool version + authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test index f1b59e986321..536b608bd2e8 100644 --- a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test @@ -30,7 +30,10 @@ nextflow_process { assertAll( { assert process.success }, { assert path(process.out.output[0][1]).linesGzip.toString().contains('[ok]') }, - { assert snapshot(process.out.versions).match() } + { assert snapshot( + path(process.out.output[0][1]).linesGzip.size(), + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } @@ -59,8 +62,11 @@ nextflow_process { { assert path(process.out.output.get(0).get(1)).linesGzip.toString().contains('[ok]') }, { assert path(process.out.target_summary.get(0).get(1)).linesGzip.toString().contains('[ok]') }, { assert snapshot( - process.out.alignments + - process.out.versions + process.out.alignments, + path(process.out.output[0][1]).linesGzip.size(), + path(process.out.target_summary[0][1]).linesGzip.size(), + path(process.out.domain_summary[0][1]).linesGzip.size(), + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -89,7 +95,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -117,7 +123,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap index e6b22771dc6c..342ad3320925 100644 --- a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap +++ b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap @@ -1,40 +1,26 @@ { "hmmer/hmmsearch": { "content": [ - [ - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" - ] + 177, + { + "versions_hmmer": [ + [ + "HMMER_HMMSEARCH", + "hmmer", + "3.4" + ] + ] + } ], + "timestamp": "2026-05-01T15:56:26.918790578", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-28T12:18:47.293093635" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "hmmer/hmmsearch - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" - ], "alignments": [ ], @@ -53,59 +39,24 @@ "target_summary": [ ], - "versions": [ - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" + "versions_hmmer": [ + [ + "HMMER_HMMSEARCH", + "hmmer", + "3.4" + ] ] } ], + "timestamp": "2026-05-01T15:56:38.131715175", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-28T12:18:57.862047944" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "hmmer/hmmsearch - optional - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sto.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" - ], "alignments": [ [ { @@ -142,16 +93,20 @@ "test.tbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" + "versions_hmmer": [ + [ + "HMMER_HMMSEARCH", + "hmmer", + "3.4" + ] ] } ], + "timestamp": "2026-05-01T15:56:43.971890326", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-28T12:19:03.49192788" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "hmmer/hmmsearch - optional": { "content": [ @@ -162,14 +117,25 @@ "single_end": false }, "test.sto.gz:md5,5c44c289b9e36aa1f7f3afae2005fbb7" - ], - "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f" - ] + ] + ], + 181, + 14, + 14, + { + "versions_hmmer": [ + [ + "HMMER_HMMSEARCH", + "hmmer", + "3.4" + ] + ] + } ], + "timestamp": "2026-05-01T15:56:32.258208367", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-28T12:18:52.725638562" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file From 72cf8eaa9c4d7ddf26cd1a18b0dcbef6ae2ebb7c Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 2 May 2026 09:21:28 +0100 Subject: [PATCH 2/5] downstream subworkflows update - removed versions --- .../fasta_hmmsearch_rank_fastas/main.nf | 1 - .../tests/main.nf.test.snap | 20 ++++++++----------- .../nf-core/fasta_newick_epang_gappa/main.nf | 4 ---- .../tests/main.nf.test.snap | 16 +++++++-------- 4 files changed, 16 insertions(+), 25 deletions(-) diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf index b53507f712a8..40cf73ef725f 100644 --- a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf @@ -18,7 +18,6 @@ workflow FASTA_HMMSEARCH_RANK_FASTAS { .set { ch_hmmsearch } HMMER_HMMSEARCH ( ch_hmmsearch ) - ch_versions = ch_versions.mix(HMMER_HMMSEARCH.out.versions.first()) HMMER_HMMSEARCH.out.target_summary .collect { index -> index[1] } diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap index efd7075d35bb..6020e49e55d4 100644 --- a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap @@ -14,7 +14,6 @@ ], "2": [ - "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" ], "hmmrank": [ @@ -29,16 +28,15 @@ ], "versions": [ - "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" ] } ], + "timestamp": "2026-05-02T09:19:34.182240068", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-12T20:13:12.239271103" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "16s_out": { "content": [ @@ -72,7 +70,6 @@ ] ], "2": [ - "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" ], "hmmrank": [ @@ -104,15 +101,14 @@ ] ], "versions": [ - "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" ] } ], + "timestamp": "2026-05-02T09:19:27.347377293", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-16T14:27:11.287820587" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf b/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf index 6341c8063461..106a9065f64b 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf @@ -44,8 +44,6 @@ workflow FASTA_NEWICK_EPANG_GAPPA { .map { it -> [ it.meta, it.data.hmmfile ] } ) - ch_versions = ch_versions.mix(HMMER_HMMBUILD.out.versions.first()) - // 1.b For entries that do not specify an hmm file, "unalign" the reference sequences before they can be aligned to the hmm. HMMER_UNALIGNREF ( ch_hmmer_data @@ -72,7 +70,6 @@ workflow FASTA_NEWICK_EPANG_GAPPA { ch_hmmer_alignref.map { it -> [ it[0], it[1][0] ] }, ch_hmmer_alignref.map { it -> it[1][1] } ) - ch_versions = ch_versions.mix(HMMER_HMMALIGNREF.out.versions) ch_hmmer_alignquery = channel.empty() .mix(ch_hmmer_data.map { it -> [ it.meta, it.data.queryseqfile ] }) @@ -83,7 +80,6 @@ workflow FASTA_NEWICK_EPANG_GAPPA { ch_hmmer_alignquery.map { it -> [ it[0], it[1][0] ] }, ch_hmmer_alignquery.map { it -> it[1][1] } ) - ch_versions = ch_versions.mix(HMMER_HMMALIGNQUERY.out.versions) // 1.d Mask the alignments (Add '--rf-is-mask' ext.args in config for the process.) HMMER_MASKREF ( HMMER_HMMALIGNREF.out.sto.map { it -> [ it[0], it[1], [], [], [], [], [], [] ] }, [] ) diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap index 3d221af5505e..d94cf3b77633 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap @@ -226,19 +226,19 @@ } }, "nucl_hmmer.versions.yml_lines": { - "content": "eafb4184937621216ff03df17c4245a6", - "timestamp": "2024-11-14T10:17:41.733022413", + "content": "664dc00d47aecd41a420dc6ba7ef4eea", + "timestamp": "2026-05-02T09:10:34.204590148", "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "hmmer.versions.yml_lines": { - "content": "eafb4184937621216ff03df17c4245a6", - "timestamp": "2024-11-14T10:16:44.884598465", + "content": "664dc00d47aecd41a420dc6ba7ef4eea", + "timestamp": "2026-05-02T09:09:26.565179143", "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "mafft.versions.yml": { From a57e90966792e3e1ce11409ac6939a5ea8fdf425 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Sat, 2 May 2026 09:37:04 +0100 Subject: [PATCH 3/5] removing versions from newick subworkflow --- .../tests/main.nf.test | 8 --- .../tests/main.nf.test.snap | 72 ------------------- 2 files changed, 80 deletions(-) diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test index 67591b3dce78..0320dcd756b1 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test @@ -57,8 +57,6 @@ nextflow_workflow { { assert snapshot(workflow.out.grafted_phylogeny.get(0).get(1)).md5().match("hmmer.graft.placement.epa_result.newick_lines") }, { assert snapshot(file(workflow.out.taxonomy_profile.get(0).get(1)).name).match("hmmer.taxonomy.profile.tsv") }, { assert snapshot(file(workflow.out.taxonomy_per_query.get(0).get(1)).name).match("hmmer.taxonomy.per_query.tsv") }, - { assert snapshot(file(workflow.out.versions.get(0)).name).match("hmmer.versions.yml") }, - { assert snapshot(workflow.out.versions.get(0)).md5().match("hmmer.versions.yml_lines") }, ) } } @@ -98,8 +96,6 @@ nextflow_workflow { { assert snapshot(workflow.out.grafted_phylogeny.get(0).get(1)).md5().match("mafft.taxonomy.profile.tsv_lines") }, { assert snapshot(file(workflow.out.taxonomy_per_query.get(0).get(1)).name).match("mafft.taxonomy.per_query.tsv") }, { assert snapshot(workflow.out.grafted_phylogeny.get(0).get(1)).md5().match("mafft.taxonomy.per_query.tsv_lines") }, - { assert snapshot(file(workflow.out.versions.get(0)).name).match("mafft.versions.yml") }, - { assert snapshot(workflow.out.versions.get(0)).md5().match("mafft.versions.yml_lines") }, ) } } @@ -134,8 +130,6 @@ nextflow_workflow { { assert snapshot(workflow.out.grafted_phylogeny.get(0).get(1)).md5().match("clustalo.graft.placement.epa_result.newick_lines") }, { assert snapshot(file(workflow.out.taxonomy_profile.get(0).get(1)).name).match("clustalo.taxonomy.profile.tsv") }, { assert snapshot(file(workflow.out.taxonomy_per_query.get(0).get(1)).name).match("clustalo.taxonomy.per_query.tsv") }, - { assert snapshot(file(workflow.out.versions.get(0)).name).match("clustalo.versions.yml") }, - { assert snapshot(workflow.out.versions.get(0)).md5().match("clustalo.versions.yml_lines") }, ) } } @@ -167,8 +161,6 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot(file(workflow.out.jplace.get(0).get(1)).name).match("nucl_hmmer.epa_result.jplace.gz") }, { assert snapshot(file(workflow.out.grafted_phylogeny.get(0).get(1)).name).match("nucl_hmmer.graft.placement.epa_result.newick") }, - { assert snapshot(file(workflow.out.versions.get(0)).name).match("nucl_hmmer.versions.yml") }, - { assert snapshot(workflow.out.versions.get(0)).md5().match("nucl_hmmer.versions.yml_lines") }, ) } } diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap index d94cf3b77633..93e94146d3fd 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap @@ -15,16 +15,6 @@ "nextflow": "23.04.5" } }, - "nucl_hmmer.versions.yml": { - "content": [ - "versions.yml" - ], - "timestamp": "2024-11-14T10:17:41.730837855", - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - } - }, "clustalo.graft.placement.epa_result.newick": { "content": [ "clustalo.graft.clustalo.epa_result.newick" @@ -75,14 +65,6 @@ "nextflow": "23.04.5" } }, - "mafft.versions.yml_lines": { - "content": "f5957093def0191f32bb294000fb9242", - "timestamp": "2024-11-14T10:16:59.988948939", - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - } - }, "clustalo.taxonomy.profile.tsv": { "content": [ "clustalo.taxonomy.profile.tsv" @@ -129,24 +111,6 @@ "nextflow": "23.04.5" } }, - "clustalo.versions.yml": { - "content": [ - "versions.yml" - ], - "timestamp": "2024-11-26T18:13:47.005413", - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" - } - }, - "clustalo.versions.yml_lines": { - "content": "f5957093def0191f32bb294000fb9242", - "timestamp": "2026-03-14T03:39:07.299263474", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, "clustalo.graft.placement.epa_result.newick_lines": { "content": "c5019b883ff08671bd71be3eb23efa52", "timestamp": "2024-11-26T19:04:43.809323", @@ -155,16 +119,6 @@ "nextflow": "24.10.1" } }, - "hmmer.versions.yml": { - "content": [ - "versions.yml" - ], - "timestamp": "2024-11-14T10:16:44.880743216", - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - } - }, "hmmer.epa_result.jplace.gz": { "content": [ "hmmer.epa_result.jplace.gz" @@ -224,31 +178,5 @@ "nf-test": "0.9.0", "nextflow": "23.04.5" } - }, - "nucl_hmmer.versions.yml_lines": { - "content": "664dc00d47aecd41a420dc6ba7ef4eea", - "timestamp": "2026-05-02T09:10:34.204590148", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - }, - "hmmer.versions.yml_lines": { - "content": "664dc00d47aecd41a420dc6ba7ef4eea", - "timestamp": "2026-05-02T09:09:26.565179143", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - }, - "mafft.versions.yml": { - "content": [ - "versions.yml" - ], - "timestamp": "2024-11-14T10:16:59.986610634", - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.04.5" - } } } \ No newline at end of file From 419d53a4de1fd2af4193d031e57ca85cd41c9113 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Tue, 5 May 2026 09:29:06 +0100 Subject: [PATCH 4/5] source containers from quay and galaxy --- modules/nf-core/hmmer/hmmalign/main.nf | 4 ++-- modules/nf-core/hmmer/hmmbuild/main.nf | 4 ++-- modules/nf-core/hmmer/hmmsearch/main.nf | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 1f9edaa30e2f..519da8623d81 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -4,8 +4,8 @@ process HMMER_HMMALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' : - 'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }" + 'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' : + 'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 1b5b263102f5..e149f5f81d25 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -4,8 +4,8 @@ process HMMER_HMMBUILD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' : - 'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }" + 'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' : + 'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }" input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 7d823b1f4141..4a1e499b3494 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -4,8 +4,8 @@ process HMMER_HMMSEARCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' : - 'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }" + 'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' : + 'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }" input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) From be0f93832b2fe01ff27ad96054c5b56f094ae694 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Fri, 8 May 2026 10:38:39 +0100 Subject: [PATCH 5/5] update versions eval command according to latest hmmsearch update --- modules/nf-core/hmmer/hmmalign/main.nf | 2 +- modules/nf-core/hmmer/hmmalign/meta.yml | 17 ++++++++--------- modules/nf-core/hmmer/hmmbuild/main.nf | 2 +- modules/nf-core/hmmer/hmmbuild/meta.yml | 17 ++++++++--------- 4 files changed, 18 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 519da8623d81..2bfb17d19c0d 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -13,7 +13,7 @@ process HMMER_HMMALIGN { output: tuple val(meta), path("*.sto.gz"), emit: sto - tuple val("${task.process}"), val("hmmer"), eval("hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer + tuple val("${task.process}"), val('hmmer'), eval("hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'"), emit: versions_hmmer, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml index 6f095a04a0ec..ecaa5b12c27a 100644 --- a/modules/nf-core/hmmer/hmmalign/meta.yml +++ b/modules/nf-core/hmmer/hmmalign/meta.yml @@ -48,25 +48,24 @@ output: versions_hmmer: - - ${task.process}: type: string - description: The process name + description: The name of the process - hmmer: type: string - description: The tool name - - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + description: The name of the tool + - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//': type: eval - description: The tool version - + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: type: string - description: The process name + description: The name of the process - hmmer: type: string - description: The tool name - - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + description: The name of the tool + - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//': type: eval - description: The tool version + description: The expression to obtain the version of the tool authors: - "@erikrikarddaniel" diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index e149f5f81d25..5227756269a9 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -14,7 +14,7 @@ process HMMER_HMMBUILD { output: tuple val(meta), path("*.hmm.gz"), emit: hmm path "*.hmmbuild.txt", emit: hmmbuildout - tuple val("${task.process}"), val("hmmer"), eval("hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer + tuple val("${task.process}"), val('hmmer'), eval("hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'"), emit: versions_hmmer, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index be03297974d9..48639997e45f 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -53,25 +53,24 @@ output: versions_hmmer: - - ${task.process}: type: string - description: The process name + description: The name of the process - hmmer: type: string - description: The tool name - - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + description: The name of the tool + - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//': type: eval - description: The tool version - + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: type: string - description: The process name + description: The name of the process - hmmer: type: string - description: The tool name - - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //': + description: The name of the tool + - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//': type: eval - description: The tool version + description: The expression to obtain the version of the tool authors: - "@erikrikarddaniel"