From 8251dcacc6d3c56238b8e39fb3e6db15e29fd3c6 Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Wed, 1 Jul 2026 15:20:29 +1000 Subject: [PATCH 1/6] update to topics, update deps and containers --- modules/nf-core/pangolin/run/environment.yml | 6 ++-- modules/nf-core/pangolin/run/main.nf | 16 ++-------- modules/nf-core/pangolin/run/meta.yml | 22 +++++++------ .../pangolin/updatedata/environment.yml | 7 ++-- modules/nf-core/pangolin/updatedata/main.nf | 19 +++-------- modules/nf-core/pangolin/updatedata/meta.yml | 32 +++++++++++++------ 6 files changed, 50 insertions(+), 52 deletions(-) diff --git a/modules/nf-core/pangolin/run/environment.yml b/modules/nf-core/pangolin/run/environment.yml index 4653a72fa0cf..49d1206d976e 100644 --- a/modules/nf-core/pangolin/run/environment.yml +++ b/modules/nf-core/pangolin/run/environment.yml @@ -3,6 +3,6 @@ channels: - bioconda dependencies: - - bioconda::pangolin=4.3.1 - - bioconda::pangolin-data=1.32 - - bioconda::snakemake=7.32.4 + - bioconda::pangolin=4.4 + - bioconda::pangolin-data=1.39 + - bioconda::snakemake-minimal=9.21.1 \ No newline at end of file diff --git a/modules/nf-core/pangolin/run/main.nf b/modules/nf-core/pangolin/run/main.nf index 21d5847a0509..b95ac2f7db02 100644 --- a/modules/nf-core/pangolin/run/main.nf +++ b/modules/nf-core/pangolin/run/main.nf @@ -4,8 +4,8 @@ process PANGOLIN_RUN { 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/sha256/5f/5f10f9bd63d24e2382406b2b348c65ae1ac74118e6eb17f5e30b310fbc1bc4b9/data' : - 'community.wave.seqera.io/library/pangolin-data_pangolin_pip_snakemake:7987089a2a044e70' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/85/858e91f6972f0d8d71dae844bf0232656f5d91112b9a5610f559659b33414c86/data' : + 'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake-minimal:638a1eb68adff9c7' }" input: tuple val(meta), path(fasta) @@ -13,7 +13,7 @@ process PANGOLIN_RUN { output: tuple val(meta), path('*.csv'), emit: report - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions when: task.ext.when == null || task.ext.when @@ -31,11 +31,6 @@ process PANGOLIN_RUN { --outfile ${prefix}.pangolin.csv \\ --threads $task.cpus \\ $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pangolin: \$(pangolin --version | sed "s/pangolin //g") - END_VERSIONS """ stub: @@ -44,10 +39,5 @@ process PANGOLIN_RUN { export XDG_CACHE_HOME=/tmp/.cache touch ${prefix}.pangolin.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pangolin: \$(pangolin --version | sed "s/pangolin //g") - END_VERSIONS """ } diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml index 2f3ea51003ff..e5739f698ad5 100644 --- a/modules/nf-core/pangolin/run/meta.yml +++ b/modules/nf-core/pangolin/run/meta.yml @@ -11,7 +11,8 @@ tools: Phylogenetic Assignment of Named Global Outbreak LINeages homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:pangolin_cov-lineages input: - - meta: @@ -39,14 +40,17 @@ output: description: Pangolin lineage report pattern: "*.{csv}" ontologies: - - edam: http://edamontology.org/format_3752 # CSV - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - edam: http://edamontology.org/format_3752 + versions_pangolin: + - - ${task.process}: + type: string + description: The name of the process + - pangolin: + type: string + description: The name of the tool + - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/pangolin/updatedata/environment.yml b/modules/nf-core/pangolin/updatedata/environment.yml index 4653a72fa0cf..383919d75168 100644 --- a/modules/nf-core/pangolin/updatedata/environment.yml +++ b/modules/nf-core/pangolin/updatedata/environment.yml @@ -1,8 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::pangolin=4.3.1 - - bioconda::pangolin-data=1.32 - - bioconda::snakemake=7.32.4 + - bioconda::pangolin=4.4 + - bioconda::pangolin-data=1.39 + - bioconda::snakemake-minimal=9.21.1 \ No newline at end of file diff --git a/modules/nf-core/pangolin/updatedata/main.nf b/modules/nf-core/pangolin/updatedata/main.nf index e4edf77ae25a..a98113c2a146 100644 --- a/modules/nf-core/pangolin/updatedata/main.nf +++ b/modules/nf-core/pangolin/updatedata/main.nf @@ -4,15 +4,16 @@ process PANGOLIN_UPDATEDATA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f10f9bd63d24e2382406b2b348c65ae1ac74118e6eb17f5e30b310fbc1bc4b9/data' : - 'community.wave.seqera.io/library/pangolin-data_pangolin_pip_snakemake:7987089a2a044e70' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/85/858e91f6972f0d8d71dae844bf0232656f5d91112b9a5610f559659b33414c86/data' : + 'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake-minimal:638a1eb68adff9c7' }" input: val(dbname) output: - path("${prefix}") , emit: db - path "versions.yml" , emit: versions + path("${prefix}") , emit: db + tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed -n 's/pangolin-data \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin_dataset, topic: versions + tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions when: task.ext.when == null || task.ext.when @@ -29,21 +30,11 @@ process PANGOLIN_UPDATEDATA { --update-data \\ --threads $task.cpus \\ --datadir ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pangolin: \$(pangolin --version | sed "s/pangolin //g") - END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${dbname}" """ mkdir -p ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pangolin: \$(pangolin --version | sed "s/pangolin //g") - END_VERSIONS """ } diff --git a/modules/nf-core/pangolin/updatedata/meta.yml b/modules/nf-core/pangolin/updatedata/meta.yml index 278a222590a9..455717ccea9e 100644 --- a/modules/nf-core/pangolin/updatedata/meta.yml +++ b/modules/nf-core/pangolin/updatedata/meta.yml @@ -24,17 +24,29 @@ output: db: - ${prefix}: type: file - description: Directory containing downloaded data with directory naming being - the user provided dbname or prefix. + description: Directory containing downloaded data with directory naming + being the user provided dbname or prefix. ontologies: [] - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_pangolin_dataset: + - - ${task.process}: + type: string + description: The name of the process + - pangolin-dataset: + type: string + description: The name of the tool + - pangolin -pv | sed -n 's/pangolin-data \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + versions_pangolin: + - - ${task.process}: + type: string + description: The name of the process + - pangolin: + type: string + description: The name of the tool + - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@Joon-Klaps" maintainers: From f42ee0f762af6b3d9731e2abebb61f95879a0eca Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Wed, 1 Jul 2026 16:05:43 +1000 Subject: [PATCH 2/6] linting; remove testing of version.yml from nf-test files --- modules/nf-core/pangolin/run/environment.yml | 6 +- modules/nf-core/pangolin/run/meta.yml | 4 +- .../nf-core/pangolin/run/tests/main.nf.test | 1 - .../pangolin/run/tests/main.nf.test.snap | 61 +++++++++++-------- .../pangolin/updatedata/environment.yml | 5 +- modules/nf-core/pangolin/updatedata/meta.yml | 25 +++++++- .../pangolin/updatedata/tests/main.nf.test | 1 - .../updatedata/tests/main.nf.test.snap | 47 +++++++++----- 8 files changed, 101 insertions(+), 49 deletions(-) diff --git a/modules/nf-core/pangolin/run/environment.yml b/modules/nf-core/pangolin/run/environment.yml index 49d1206d976e..bd814ab03696 100644 --- a/modules/nf-core/pangolin/run/environment.yml +++ b/modules/nf-core/pangolin/run/environment.yml @@ -1,8 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::pangolin=4.4 - bioconda::pangolin-data=1.39 - - bioconda::snakemake-minimal=9.21.1 \ No newline at end of file + - bioconda::pangolin=4.4 + - bioconda::snakemake-minimal=9.21.1 diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml index e5739f698ad5..c805ac008128 100644 --- a/modules/nf-core/pangolin/run/meta.yml +++ b/modules/nf-core/pangolin/run/meta.yml @@ -28,7 +28,6 @@ input: type: directory description: | Directory containing the Pangolin database - output: report: - - meta: @@ -41,7 +40,8 @@ output: pattern: "*.{csv}" ontologies: - edam: http://edamontology.org/format_3752 - versions_pangolin: +topics: + versions: - - ${task.process}: type: string description: The name of the process diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test b/modules/nf-core/pangolin/run/tests/main.nf.test index 519f01b0b9b4..fa5dbdb6bd35 100644 --- a/modules/nf-core/pangolin/run/tests/main.nf.test +++ b/modules/nf-core/pangolin/run/tests/main.nf.test @@ -63,7 +63,6 @@ nextflow_process { { assert path(process.out.report[0][1]).readLines().first().contains("taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note") }, { assert snapshot( file(process.out.report[0][1]).name, - process.out.versions ).match() } ) diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test.snap b/modules/nf-core/pangolin/run/tests/main.nf.test.snap index 04057e5abd1d..92d9b3d75a30 100644 --- a/modules/nf-core/pangolin/run/tests/main.nf.test.snap +++ b/modules/nf-core/pangolin/run/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e" + [ + "PANGOLIN_RUN", + "pangolin", + "4.4" + ] ], "report": [ [ @@ -21,29 +25,30 @@ "test.pangolin.csv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e" + "versions_pangolin": [ + [ + "PANGOLIN_RUN", + "pangolin", + "4.4" + ] ] } ], + "timestamp": "2026-07-01T15:40:11.850894785", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T11:10:47.50504972" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "sarscov2 genome [fasta] - update data": { "content": [ - "test.pangolin.csv", - [ - "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e" - ] + "test.pangolin.csv" ], + "timestamp": "2026-07-01T15:58:42.989095116", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T11:10:27.540927677" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "sarscov2 genome [fasta]": { "content": [ @@ -53,29 +58,37 @@ { "id": "test" }, - "test.pangolin.csv:md5,876b3d5cb0f2b438cb62931b81bb0c8c" + "test.pangolin.csv:md5,bdcdb7bcec59c2e6a12c11ac7ce43b09" ] ], "1": [ - "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e" + [ + "PANGOLIN_RUN", + "pangolin", + "4.4" + ] ], "report": [ [ { "id": "test" }, - "test.pangolin.csv:md5,876b3d5cb0f2b438cb62931b81bb0c8c" + "test.pangolin.csv:md5,bdcdb7bcec59c2e6a12c11ac7ce43b09" ] ], - "versions": [ - "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e" + "versions_pangolin": [ + [ + "PANGOLIN_RUN", + "pangolin", + "4.4" + ] ] } ], + "timestamp": "2026-07-01T15:39:37.743772028", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T11:09:22.593905868" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/pangolin/updatedata/environment.yml b/modules/nf-core/pangolin/updatedata/environment.yml index 383919d75168..bd814ab03696 100644 --- a/modules/nf-core/pangolin/updatedata/environment.yml +++ b/modules/nf-core/pangolin/updatedata/environment.yml @@ -1,9 +1,10 @@ +--- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::pangolin=4.4 - bioconda::pangolin-data=1.39 - - bioconda::snakemake-minimal=9.21.1 \ No newline at end of file + - bioconda::pangolin=4.4 + - bioconda::snakemake-minimal=9.21.1 diff --git a/modules/nf-core/pangolin/updatedata/meta.yml b/modules/nf-core/pangolin/updatedata/meta.yml index 455717ccea9e..4c36c192c2a9 100644 --- a/modules/nf-core/pangolin/updatedata/meta.yml +++ b/modules/nf-core/pangolin/updatedata/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: pangolin_updatedata description: Phylogenetic Assignment of Named Global Outbreak LINeages keywords: @@ -13,9 +12,9 @@ tools: Phylogenetic Assignment of Named Global Outbreak LINeages homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:pangolin_cov-lineages - input: - dbname: type: string @@ -47,6 +46,26 @@ output: - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': type: eval description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - pangolin-dataset: + type: string + description: The name of the tool/dataset + - pangolin -pv | sed -n 's/pangolin-data \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - pangolin: + type: string + description: The name of the tool + - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test b/modules/nf-core/pangolin/updatedata/tests/main.nf.test index 7d7dcaf0c622..33545fdc7383 100644 --- a/modules/nf-core/pangolin/updatedata/tests/main.nf.test +++ b/modules/nf-core/pangolin/updatedata/tests/main.nf.test @@ -25,7 +25,6 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.db[0].toString()).listFiles().collect { it.name }.toSorted(), // A mix of empty and non-empty files - process.out.versions ).match() } ) diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap b/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap index be43bc7b1ff9..92faab36a695 100644 --- a/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap +++ b/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap @@ -3,16 +3,13 @@ "content": [ [ - ], - [ - "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc" ] ], + "timestamp": "2026-07-01T15:53:01.070936935", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T11:36:25.100043271" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "str - testdb - stub": { "content": [ @@ -23,22 +20,44 @@ ] ], "1": [ - "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc" + [ + "PANGOLIN_UPDATEDATA", + "pangolin-dataset", + "1.39" + ] + ], + "2": [ + [ + "PANGOLIN_UPDATEDATA", + "pangolin", + "4.4" + ] ], "db": [ [ ] ], - "versions": [ - "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc" + "versions_pangolin": [ + [ + "PANGOLIN_UPDATEDATA", + "pangolin", + "4.4" + ] + ], + "versions_pangolin_dataset": [ + [ + "PANGOLIN_UPDATEDATA", + "pangolin-dataset", + "1.39" + ] ] } ], + "timestamp": "2026-07-01T15:48:29.858896074", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T11:36:28.859501307" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file From ce207271c4da7f2a98edb3a7eedf9c1534f39182 Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Wed, 1 Jul 2026 16:52:27 +1000 Subject: [PATCH 3/6] fix meta file --- modules/nf-core/pangolin/run/meta.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml index c805ac008128..74fdb2a80ad3 100644 --- a/modules/nf-core/pangolin/run/meta.yml +++ b/modules/nf-core/pangolin/run/meta.yml @@ -40,6 +40,16 @@ output: pattern: "*.{csv}" ontologies: - edam: http://edamontology.org/format_3752 + versions_pangolin: + - - ${task.process}: + type: string + description: The name of the process + - pangolin: + type: string + description: The name of the tool + - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: From 533c4b7bd8a10757da2577ad7ca39a527b31d256 Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Mon, 20 Jul 2026 13:55:15 +1000 Subject: [PATCH 4/6] implement reviewer comments --- modules/nf-core/pangolin/run/main.nf | 2 +- modules/nf-core/pangolin/run/meta.yml | 2 +- .../nf-core/pangolin/run/tests/main.nf.test | 6 ++--- .../pangolin/run/tests/main.nf.test.snap | 24 ++++++++++++++--- modules/nf-core/pangolin/updatedata/main.nf | 2 +- .../pangolin/updatedata/tests/main.nf.test | 5 +--- .../updatedata/tests/main.nf.test.snap | 26 ++++++++++++++++--- 7 files changed, 48 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/pangolin/run/main.nf b/modules/nf-core/pangolin/run/main.nf index b95ac2f7db02..826c0bc22ba0 100644 --- a/modules/nf-core/pangolin/run/main.nf +++ b/modules/nf-core/pangolin/run/main.nf @@ -13,7 +13,7 @@ process PANGOLIN_RUN { output: tuple val(meta), path('*.csv'), emit: report - tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions + tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed 's/pangolin //'"), emit: versions_pangolin, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml index 74fdb2a80ad3..236ae5b54168 100644 --- a/modules/nf-core/pangolin/run/meta.yml +++ b/modules/nf-core/pangolin/run/meta.yml @@ -39,7 +39,7 @@ output: description: Pangolin lineage report pattern: "*.{csv}" ontologies: - - edam: http://edamontology.org/format_3752 + - edam: http://edamontology.org/format_3752 #CSV versions_pangolin: - - ${task.process}: type: string diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test b/modules/nf-core/pangolin/run/tests/main.nf.test index fa5dbdb6bd35..3c7a6443105a 100644 --- a/modules/nf-core/pangolin/run/tests/main.nf.test +++ b/modules/nf-core/pangolin/run/tests/main.nf.test @@ -61,10 +61,8 @@ nextflow_process { assertAll( { assert process.success }, { assert path(process.out.report[0][1]).readLines().first().contains("taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note") }, - { assert snapshot( - file(process.out.report[0][1]).name, - ).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["report"])).match() } + ) } } diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test.snap b/modules/nf-core/pangolin/run/tests/main.nf.test.snap index 92d9b3d75a30..0b22ca051f15 100644 --- a/modules/nf-core/pangolin/run/tests/main.nf.test.snap +++ b/modules/nf-core/pangolin/run/tests/main.nf.test.snap @@ -34,7 +34,7 @@ ] } ], - "timestamp": "2026-07-01T15:40:11.850894785", + "timestamp": "2026-07-20T11:54:15.284245093", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" @@ -42,9 +42,25 @@ }, "sarscov2 genome [fasta] - update data": { "content": [ - "test.pangolin.csv" + { + "report": [ + [ + { + "id": "test" + }, + "test.pangolin.csv" + ] + ], + "versions_pangolin": [ + [ + "PANGOLIN_RUN", + "pangolin", + "4.4" + ] + ] + } ], - "timestamp": "2026-07-01T15:58:42.989095116", + "timestamp": "2026-07-20T11:58:12.906874243", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" @@ -85,7 +101,7 @@ ] } ], - "timestamp": "2026-07-01T15:39:37.743772028", + "timestamp": "2026-07-20T11:53:38.602007683", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" diff --git a/modules/nf-core/pangolin/updatedata/main.nf b/modules/nf-core/pangolin/updatedata/main.nf index a98113c2a146..b86912bcb0e5 100644 --- a/modules/nf-core/pangolin/updatedata/main.nf +++ b/modules/nf-core/pangolin/updatedata/main.nf @@ -13,7 +13,7 @@ process PANGOLIN_UPDATEDATA { output: path("${prefix}") , emit: db tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed -n 's/pangolin-data \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin_dataset, topic: versions - tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions + tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed 's/pangolin //'"), emit: versions_pangolin, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test b/modules/nf-core/pangolin/updatedata/tests/main.nf.test index 33545fdc7383..a2c2dfb079e2 100644 --- a/modules/nf-core/pangolin/updatedata/tests/main.nf.test +++ b/modules/nf-core/pangolin/updatedata/tests/main.nf.test @@ -23,10 +23,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.db[0].toString()).listFiles().collect { it.name }.toSorted(), // A mix of empty and non-empty files - ).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["report"])).match() } ) } } diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap b/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap index 92faab36a695..5f20776771e7 100644 --- a/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap +++ b/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap @@ -1,11 +1,29 @@ { "str - testdb": { "content": [ - [ - - ] + { + "db": [ + [ + + ] + ], + "versions_pangolin": [ + [ + "PANGOLIN_UPDATEDATA", + "pangolin", + "4.4" + ] + ], + "versions_pangolin_dataset": [ + [ + "PANGOLIN_UPDATEDATA", + "pangolin-dataset", + "1.39" + ] + ] + } ], - "timestamp": "2026-07-01T15:53:01.070936935", + "timestamp": "2026-07-20T13:51:58.011686701", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" From 1e535e3d92c15a962884e9798baa140774938974 Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Mon, 20 Jul 2026 15:48:09 +1000 Subject: [PATCH 5/6] linting update --- modules/nf-core/pangolin/run/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml index 236ae5b54168..e5649e40bd2a 100644 --- a/modules/nf-core/pangolin/run/meta.yml +++ b/modules/nf-core/pangolin/run/meta.yml @@ -47,7 +47,7 @@ output: - pangolin: type: string description: The name of the tool - - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + - pangolin -v | sed 's/pangolin //': type: eval description: The expression to obtain the version of the tool topics: @@ -58,7 +58,7 @@ topics: - pangolin: type: string description: The name of the tool - - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + - pangolin -v | sed 's/pangolin //': type: eval description: The expression to obtain the version of the tool authors: From d69f3744135eb56a9de40f133d143da504d52fd9 Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Mon, 20 Jul 2026 16:02:18 +1000 Subject: [PATCH 6/6] linting --- modules/nf-core/pangolin/updatedata/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/pangolin/updatedata/meta.yml b/modules/nf-core/pangolin/updatedata/meta.yml index 4c36c192c2a9..86f143b27a2f 100644 --- a/modules/nf-core/pangolin/updatedata/meta.yml +++ b/modules/nf-core/pangolin/updatedata/meta.yml @@ -43,7 +43,7 @@ output: - pangolin: type: string description: The name of the tool - - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + - pangolin -v | sed 's/pangolin //': type: eval description: The expression to obtain the version of the tool topics: @@ -63,7 +63,7 @@ topics: - pangolin: type: string description: The name of the tool - - pangolin -v | sed -n 's/pangolin \([0-9.]*\).*/\1/p': + - pangolin -v | sed 's/pangolin //': type: eval description: The expression to obtain the version of the tool authors: