From e7e07c3d116befb9b13373d4bea0013efad29fb5 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Thu, 22 Jan 2026 13:05:04 +0000 Subject: [PATCH 1/6] update to new versions capture for checkm2 databasedownload and checkm2 predict --- .../nf-core/checkm2/databasedownload/main.nf | 14 ++------- .../nf-core/checkm2/databasedownload/meta.yml | 30 +++++++++++++------ .../databasedownload/tests/main.nf.test.snap | 24 +++++---------- modules/nf-core/checkm2/predict/main.nf | 24 ++++----------- modules/nf-core/checkm2/predict/meta.yml | 29 +++++++++++++----- .../checkm2/predict/tests/main.nf.test | 16 +++++----- .../checkm2/predict/tests/main.nf.test.snap | 20 +++++-------- .../checkm2/predict/tests/nextflow.config | 2 +- 8 files changed, 75 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/checkm2/databasedownload/main.nf b/modules/nf-core/checkm2/databasedownload/main.nf index 3b6e85b2dce8..79484d679dc0 100644 --- a/modules/nf-core/checkm2/databasedownload/main.nf +++ b/modules/nf-core/checkm2/databasedownload/main.nf @@ -24,13 +24,13 @@ process CHECKM2_DATABASEDOWNLOAD { output: tuple val(meta), path("checkm2_db_v${db_version}.dmnd"), emit: database - path("versions.yml") , emit: versions + tuple val("${task.process}"), val('aria2'), eval('aria2c --version 2>&1 | head -n 1 | cut -f3 -d " "'), topic: versions, emit: versions_checkm2_databasedownload when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '--user-agent="Wget/1.21.4"' // Modify to wget - default user agent gets blocked by zenodo. Enables users to overwrite --user-agent zenodo_id = db_zenodo_id ?: 14897628 // Default to version 3 if no ID provided api_data = downloadZenodoApiEntry(zenodo_id) db_version = api_data.metadata.version @@ -47,11 +47,6 @@ process CHECKM2_DATABASEDOWNLOAD { tar -xzf checkm2_database.tar.gz db_path=\$(find -name *.dmnd) mv \$db_path checkm2_db_v${db_version}.dmnd - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ') - END_VERSIONS """ stub: @@ -59,10 +54,5 @@ process CHECKM2_DATABASEDOWNLOAD { meta = [id: 'checkm2_db', version: db_version] """ touch checkm2_db_v${db_version}.dmnd - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ') - END_VERSIONS """ } diff --git a/modules/nf-core/checkm2/databasedownload/meta.yml b/modules/nf-core/checkm2/databasedownload/meta.yml index f91104ade216..0ac3667d8a04 100644 --- a/modules/nf-core/checkm2/databasedownload/meta.yml +++ b/modules/nf-core/checkm2/databasedownload/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkm2_databasedownload" description: CheckM2 database download keywords: @@ -16,12 +15,10 @@ tools: doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] identifier: "" - input: - db_zenodo_id: type: integer description: Zenodo ID of the CheckM2 database to download - output: database: - - meta: @@ -34,12 +31,27 @@ output: description: CheckM2 database file pattern: "checkm2_db_v*.dmnd" ontologies: [] + versions_checkm2_databasedownload: + - - ${task.process}: + type: string + description: The process the versions were collected from + - aria2: + type: string + description: The tool name + - aria2c --version 2>&1 | head -n 1 | cut -f3 -d " ": + type: string + description: The command used to generate 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 + - - ${task.process}: + type: string + description: The process the versions were collected from + - aria2: + type: string + description: The tool name + - 'aria2c --version 2>&1 | head -n 1 | cut -f3 -d " "': + type: string + description: The command used to generate the version of the tool authors: - "@dialvarezs" + - "@eit-maxlcummins" diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap index 4b0f8372e62b..3935ce15287f 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap @@ -1,26 +1,18 @@ { "test_checkm2_databasedownload": { - "content": [ - [ - "versions.yml:md5,74b6560ab3e6bae88ae53cb8ae3c283e" - ] - ], + "content": null, "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-03-13T21:41:14.428719466" + "timestamp": "2026-01-22T13:00:53.777478304" }, "test_checkm2_databasedownload - stub": { - "content": [ - [ - "versions.yml:md5,74b6560ab3e6bae88ae53cb8ae3c283e" - ] - ], + "content": null, "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-03-13T21:41:24.118075242" + "timestamp": "2026-01-22T13:01:01.263330506" } } \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/main.nf b/modules/nf-core/checkm2/predict/main.nf index dda172f92f17..8645245f2800 100644 --- a/modules/nf-core/checkm2/predict/main.nf +++ b/modules/nf-core/checkm2/predict/main.nf @@ -3,18 +3,18 @@ process CHECKM2_PREDICT { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0af812c983aeffc99c0fca9ed2c910816b2ddb9a9d0dcad7b87dab0c9c08a16f/data' - : 'community.wave.seqera.io/library/checkm2:1.1.0--60f287bc25d7a10d'}" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0af812c983aeffc99c0fca9ed2c910816b2ddb9a9d0dcad7b87dab0c9c08a16f/data': + 'community.wave.seqera.io/library/checkm2:1.1.0--60f287bc25d7a10d' }" input: tuple val(meta), path(fasta, stageAs: "input_bins/*") tuple val(dbmeta), path(db) output: - tuple val(meta), path("${prefix}"), emit: checkm2_output + tuple val(meta), path("${prefix}") , emit: checkm2_output tuple val(meta), path("${prefix}_checkm2_report.tsv"), emit: checkm2_tsv - path ("versions.yml"), emit: versions + tuple val("${task.process}"), val('checkm2'), eval('checkm2 --version'), topic: versions, emit: versions_checkm2_predict when: task.ext.when == null || task.ext.when @@ -23,22 +23,15 @@ process CHECKM2_PREDICT { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ - export DB=\$(find -L . -name "*.dmnd" -type f) - checkm2 \\ predict \\ --input ${fasta} \\ --output-directory ${prefix} \\ --threads ${task.cpus} \\ - --database_path \$DB \\ + --database_path ${db} \\ ${args} cp ${prefix}/quality_report.tsv ${prefix}_checkm2_report.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - checkm2: \$(checkm2 --version) - END_VERSIONS """ stub: @@ -46,10 +39,5 @@ process CHECKM2_PREDICT { """ mkdir ${prefix}/ touch ${prefix}_checkm2_report.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - checkm2: \$(checkm2 --version) - END_VERSIONS """ } diff --git a/modules/nf-core/checkm2/predict/meta.yml b/modules/nf-core/checkm2/predict/meta.yml index acbd65900ab1..f6cf723196c5 100644 --- a/modules/nf-core/checkm2/predict/meta.yml +++ b/modules/nf-core/checkm2/predict/meta.yml @@ -16,7 +16,6 @@ tools: doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] identifier: "" - input: - - meta: type: map @@ -37,6 +36,7 @@ input: type: file description: CheckM2 database ontologies: [] + output: checkm2_output: - - meta: @@ -60,12 +60,27 @@ output: pattern: "*.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV + versions_checkm2_predict: + - - ${task.process}: + type: string + description: The name of the process + - checkm2: + type: string + description: The name of the tool + - "checkm2 --version": + 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 process the versions were collected from + - checkm2: + type: string + description: The tool name + - "checkm2 --version": + type: string + description: The command used to generate the version of the tool authors: - "@dialvarezs" + - "@eit-maxlcummins" diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test index eeaa79934caa..fbaf4a18945e 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test @@ -5,18 +5,16 @@ nextflow_process { tag "modules" tag "checkm2" tag "checkm2/predict" - tag "untar" + tag "checkm2/databasedownload" script "modules/nf-core/checkm2/predict/main.nf" process "CHECKM2_PREDICT" setup { - run("UNTAR") { - script "../../../untar/main.nf" + run("CHECKM2_DATABASEDOWNLOAD") { + script "../../databasedownload/main.nf" process { """ - input[0] = channel - .fromPath("https://zenodo.org/records/14897628/files/checkm2_database.tar.gz", checkIfExists: true) - .map { dbfile -> [ [id: 'checkm2db'], dbfile ] } + input[0] = [] """ } } @@ -31,7 +29,7 @@ nextflow_process { process { """ input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)] ] - input[1] = UNTAR.out.untar + input[1] = CHECKM2_DATABASEDOWNLOAD.out.database """ } } @@ -55,7 +53,7 @@ nextflow_process { process { """ input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)] ] - input[1] = UNTAR.out.untar + input[1] = CHECKM2_DATABASEDOWNLOAD.out.database """ } } @@ -67,4 +65,4 @@ nextflow_process { ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap index 2fcbf50bce1c..2a4c48e4d2ea 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap @@ -9,15 +9,13 @@ "test_checkm2_report.tsv:md5,1b6021262d336b21f526d8369f6ddd3f" ] ], - [ - "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" - ] + null ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-03-13T15:23:26.857419645" + "timestamp": "2026-01-22T12:10:49.415804877" }, "test_checkm2_predict - stub": { "content": [ @@ -29,14 +27,12 @@ "test_checkm2_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" - ] + null ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-03-13T15:23:40.153127645" + "timestamp": "2026-01-22T12:10:59.525356716" } } \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/tests/nextflow.config b/modules/nf-core/checkm2/predict/tests/nextflow.config index c6248b490a40..05da5a143738 100644 --- a/modules/nf-core/checkm2/predict/tests/nextflow.config +++ b/modules/nf-core/checkm2/predict/tests/nextflow.config @@ -2,4 +2,4 @@ process { withName: "CHECKM2_PREDICT" { ext.args = "--lowmem" } -} +} \ No newline at end of file From 9539272a18cfdcd410591ff3643133bcc398c068 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 23 Jan 2026 09:28:43 +0000 Subject: [PATCH 2/6] update tests and snapshots for topic versions --- .../databasedownload/tests/main.nf.test | 4 +-- .../databasedownload/tests/main.nf.test.snap | 28 ++++++++++++++++--- .../checkm2/predict/tests/main.nf.test | 4 +-- .../checkm2/predict/tests/main.nf.test.snap | 24 +++++++++++++--- 4 files changed, 48 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test index dfeb2335adea..642dcc3aedc6 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test @@ -21,7 +21,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }, ) } @@ -42,7 +42,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }, ) } diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap index 3935ce15287f..92e6496f7595 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap @@ -1,18 +1,38 @@ { "test_checkm2_databasedownload": { - "content": null, + "content": [ + { + "versions_checkm2_databasedownload": [ + [ + "CHECKM2_DATABASEDOWNLOAD", + "aria2", + "1.37.0" + ] + ] + } + ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T13:00:53.777478304" + "timestamp": "2026-01-23T09:04:29.73758792" }, "test_checkm2_databasedownload - stub": { - "content": null, + "content": [ + { + "versions_checkm2_databasedownload": [ + [ + "CHECKM2_DATABASEDOWNLOAD", + "aria2", + "1.37.0" + ] + ] + } + ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T13:01:01.263330506" + "timestamp": "2026-01-23T09:04:35.505821639" } } \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test index fbaf4a18945e..41abb6367c59 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test @@ -37,7 +37,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.checkm2_tsv, process.out.versions).match() } + { assert snapshot(process.out.checkm2_tsv, process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -61,7 +61,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.checkm2_tsv, process.out.versions).match() } + { assert snapshot(process.out.checkm2_tsv, process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap index 2a4c48e4d2ea..2ed2ef4d29d0 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap @@ -9,13 +9,21 @@ "test_checkm2_report.tsv:md5,1b6021262d336b21f526d8369f6ddd3f" ] ], - null + { + "versions_checkm2_predict": [ + [ + "CHECKM2_PREDICT", + "checkm2", + "1.1.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T12:10:49.415804877" + "timestamp": "2026-01-23T09:28:00.364406628" }, "test_checkm2_predict - stub": { "content": [ @@ -27,12 +35,20 @@ "test_checkm2_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - null + { + "versions_checkm2_predict": [ + [ + "CHECKM2_PREDICT", + "checkm2", + "1.1.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T12:10:59.525356716" + "timestamp": "2026-01-23T09:28:10.0910672" } } \ No newline at end of file From 210723ee010f227300b419ccf310b2578b25eb63 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 23 Jan 2026 09:33:18 +0000 Subject: [PATCH 3/6] add trailing linebreak to test nextflow.config --- modules/nf-core/checkm2/predict/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/checkm2/predict/tests/nextflow.config b/modules/nf-core/checkm2/predict/tests/nextflow.config index 05da5a143738..c6248b490a40 100644 --- a/modules/nf-core/checkm2/predict/tests/nextflow.config +++ b/modules/nf-core/checkm2/predict/tests/nextflow.config @@ -2,4 +2,4 @@ process { withName: "CHECKM2_PREDICT" { ext.args = "--lowmem" } -} \ No newline at end of file +} From 7326d8dbd44325bff6a070e041186348deecb31b Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 23 Jan 2026 09:35:53 +0000 Subject: [PATCH 4/6] add trailing linebreak to main.nf.test --- modules/nf-core/checkm2/predict/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test index 41abb6367c59..85fc67307b9e 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test @@ -65,4 +65,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} From f20d7c3c5cbaf1d8ae2895f74079053c0ec1dcab Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 23 Jan 2026 16:03:57 +0000 Subject: [PATCH 5/6] fix args function to prevent issues where users provide args but not --user-agent and jobs fail --- modules/nf-core/checkm2/databasedownload/main.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/checkm2/databasedownload/main.nf b/modules/nf-core/checkm2/databasedownload/main.nf index 79484d679dc0..d8fb16eaea43 100644 --- a/modules/nf-core/checkm2/databasedownload/main.nf +++ b/modules/nf-core/checkm2/databasedownload/main.nf @@ -30,7 +30,11 @@ process CHECKM2_DATABASEDOWNLOAD { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '--user-agent="Wget/1.21.4"' // Modify to wget - default user agent gets blocked by zenodo. Enables users to overwrite --user-agent + def args = task.ext.args ?: '' + // Append user-agent if not already present + if( !args.contains('--user-agent') ) { + args = args ? "${args} --user-agent=\"Wget/1.21.4\"" : '--user-agent="Wget/1.21.4"' + } zenodo_id = db_zenodo_id ?: 14897628 // Default to version 3 if no ID provided api_data = downloadZenodoApiEntry(zenodo_id) db_version = api_data.metadata.version From d2c197acba601405534e180597a043c04a5514e1 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 30 Jan 2026 13:14:25 +0000 Subject: [PATCH 6/6] update checkm2 tests and snaps, and galah test and snaps - uses checkm2 for setup in tests --- modules/nf-core/checkm2/databasedownload/main.nf | 3 +++ .../nf-core/checkm2/databasedownload/tests/main.nf.test | 8 ++++++-- .../checkm2/databasedownload/tests/main.nf.test.snap | 2 +- modules/nf-core/checkm2/predict/tests/main.nf.test.snap | 2 +- modules/nf-core/galah/tests/main.nf.test | 4 +++- modules/nf-core/galah/tests/main.nf.test.snap | 6 +++--- 6 files changed, 17 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/checkm2/databasedownload/main.nf b/modules/nf-core/checkm2/databasedownload/main.nf index d8fb16eaea43..bf9df9c57a0c 100644 --- a/modules/nf-core/checkm2/databasedownload/main.nf +++ b/modules/nf-core/checkm2/databasedownload/main.nf @@ -51,6 +51,9 @@ process CHECKM2_DATABASEDOWNLOAD { tar -xzf checkm2_database.tar.gz db_path=\$(find -name *.dmnd) mv \$db_path checkm2_db_v${db_version}.dmnd + + # cleanup + rm -f checkm2_database.tar.gz """ stub: diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test index 642dcc3aedc6..e65378eb1561 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test @@ -21,7 +21,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }, + { assert path(process.out.database.get(0).get(1)).exists() }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith('versions') }).match() }, ) } @@ -42,7 +44,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }, + { assert path(process.out.database.get(0).get(1)).exists() }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith('versions') }).match() }, ) } diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap index 92e6496f7595..8ee778342a11 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap @@ -33,6 +33,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:04:35.505821639" + "timestamp": "2026-01-29T15:49:13.916311854" } } \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap index 2ed2ef4d29d0..0c25a0af035f 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap @@ -23,7 +23,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:28:00.364406628" + "timestamp": "2026-01-30T09:44:45.556228913" }, "test_checkm2_predict - stub": { "content": [ diff --git a/modules/nf-core/galah/tests/main.nf.test b/modules/nf-core/galah/tests/main.nf.test index 4525f75e2c95..b091f8631069 100644 --- a/modules/nf-core/galah/tests/main.nf.test +++ b/modules/nf-core/galah/tests/main.nf.test @@ -61,7 +61,9 @@ nextflow_process { [file("https://github.com/nf-core/test-datasets/raw/refs/heads/magmap/testdata/GCA_002688505.1_ASM268850v1_genomic.fna.gz", checkIfExists: true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/magmap/testdata/GCF_004296495.1_ASM429649v1_genomic.fna.gz", checkIfExists: true)] ] - input[1] = UNTAR.out.untar + input[1] = UNTAR.out.untar.map { meta, dir -> + [ [id: 'checkm2db'], file("\${dir}/*.dmnd")] + } """ } } diff --git a/modules/nf-core/galah/tests/main.nf.test.snap b/modules/nf-core/galah/tests/main.nf.test.snap index 621915548142..b1732a712ad6 100644 --- a/modules/nf-core/galah/tests/main.nf.test.snap +++ b/modules/nf-core/galah/tests/main.nf.test.snap @@ -49,10 +49,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-13T15:03:55.475991521" + "timestamp": "2026-01-26T09:42:27.663340879" }, "genomes - stub": { "content": [