From 12e0fe92db7b60a65c3ee2eb3cec9b9eb20def63 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Thu, 4 Dec 2025 17:01:39 +0000 Subject: [PATCH 1/6] rebase - git pull --rebase upstream master - merge conflicts --- modules/nf-core/trinity/main.nf | 4 + .../nf-core/trinity/tests/main.nf.test.snap | 83 +++++++++++++++++++ 2 files changed, 87 insertions(+) diff --git a/modules/nf-core/trinity/main.nf b/modules/nf-core/trinity/main.nf index 3ac485867eee..3e237f1029ab 100644 --- a/modules/nf-core/trinity/main.nf +++ b/modules/nf-core/trinity/main.nf @@ -14,7 +14,11 @@ process TRINITY { output: tuple val(meta), path("*.fa.gz") , emit: transcript_fasta tuple val(meta), path("*.log") , emit: log +<<<<<<< HEAD tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'"), topic: versions, emit: versions_trinity +======= + tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-v//'"), topic: versions, emit: versions_trinity +>>>>>>> f7b682862 (add versions topic to trinity module) when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/trinity/tests/main.nf.test.snap b/modules/nf-core/trinity/tests/main.nf.test.snap index 4c25527748c7..b643c466de66 100644 --- a/modules/nf-core/trinity/tests/main.nf.test.snap +++ b/modules/nf-core/trinity/tests/main.nf.test.snap @@ -1,5 +1,40 @@ { "homo_sapiens-test_rnaseq-paired-multiple": { +<<<<<<< HEAD +======= + "content": null, + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-10-28T11:03:10.410785664" + }, + "homo_sapiens-test_rnaseq-single": { + "content": null, + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-10-28T11:00:59.632497408" + }, + "homo_sapiens-test_rnaseq-paired": { + "content": null, + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-10-28T11:00:54.859699064" + }, + "homo_sapiens-test_rnaseq-single-multiple": { + "content": null, + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-10-28T11:03:46.654707739" + }, + "homo_sapiens-test_rnaseq-stub": { +>>>>>>> f7b682862 (add versions topic to trinity module) "content": [ { "versions_trinity": [ @@ -8,6 +43,50 @@ "trinity", "2.15.2" ] +<<<<<<< HEAD +======= + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + "TRINITY", + "trinity", + "2.15.2" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_trinity": [ + [ + "TRINITY", + "trinity", + "2.15.2" + ] +>>>>>>> f7b682862 (add versions topic to trinity module) ] } ], @@ -15,6 +94,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, +<<<<<<< HEAD "timestamp": "2025-10-28T13:22:02.72961086" }, "homo_sapiens-test_rnaseq-single": { @@ -88,5 +168,8 @@ "nextflow": "25.04.6" }, "timestamp": "2025-10-28T13:49:50.612026008" +======= + "timestamp": "2025-10-28T12:05:29.82401984" +>>>>>>> f7b682862 (add versions topic to trinity module) } } \ No newline at end of file From 526467b7a7b2dcb7e5a22bd77ac478365e9cf74d Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Tue, 28 Oct 2025 13:28:39 +0000 Subject: [PATCH 2/6] add missing test for main.nf.test --- .../nf-core/trinity/tests/main.nf.test.snap | 83 ------------------- 1 file changed, 83 deletions(-) diff --git a/modules/nf-core/trinity/tests/main.nf.test.snap b/modules/nf-core/trinity/tests/main.nf.test.snap index b643c466de66..4c25527748c7 100644 --- a/modules/nf-core/trinity/tests/main.nf.test.snap +++ b/modules/nf-core/trinity/tests/main.nf.test.snap @@ -1,40 +1,5 @@ { "homo_sapiens-test_rnaseq-paired-multiple": { -<<<<<<< HEAD -======= - "content": null, - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-10-28T11:03:10.410785664" - }, - "homo_sapiens-test_rnaseq-single": { - "content": null, - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-10-28T11:00:59.632497408" - }, - "homo_sapiens-test_rnaseq-paired": { - "content": null, - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-10-28T11:00:54.859699064" - }, - "homo_sapiens-test_rnaseq-single-multiple": { - "content": null, - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-10-28T11:03:46.654707739" - }, - "homo_sapiens-test_rnaseq-stub": { ->>>>>>> f7b682862 (add versions topic to trinity module) "content": [ { "versions_trinity": [ @@ -43,50 +8,6 @@ "trinity", "2.15.2" ] -<<<<<<< HEAD -======= - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "TRINITY", - "trinity", - "2.15.2" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "transcript_fasta": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_trinity": [ - [ - "TRINITY", - "trinity", - "2.15.2" - ] ->>>>>>> f7b682862 (add versions topic to trinity module) ] } ], @@ -94,7 +15,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, -<<<<<<< HEAD "timestamp": "2025-10-28T13:22:02.72961086" }, "homo_sapiens-test_rnaseq-single": { @@ -168,8 +88,5 @@ "nextflow": "25.04.6" }, "timestamp": "2025-10-28T13:49:50.612026008" -======= - "timestamp": "2025-10-28T12:05:29.82401984" ->>>>>>> f7b682862 (add versions topic to trinity module) } } \ No newline at end of file From 3cacf339c4b1f07ba230a818a62dfbe07b2ff829 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Tue, 28 Oct 2025 13:51:26 +0000 Subject: [PATCH 3/6] simplify string replacement for trinity version eval to remove use of colons - avoids potential yml clash --- modules/nf-core/trinity/main.nf | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/modules/nf-core/trinity/main.nf b/modules/nf-core/trinity/main.nf index 3e237f1029ab..78e741f5d84d 100644 --- a/modules/nf-core/trinity/main.nf +++ b/modules/nf-core/trinity/main.nf @@ -14,11 +14,7 @@ process TRINITY { output: tuple val(meta), path("*.fa.gz") , emit: transcript_fasta tuple val(meta), path("*.log") , emit: log -<<<<<<< HEAD tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'"), topic: versions, emit: versions_trinity -======= - tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-v//'"), topic: versions, emit: versions_trinity ->>>>>>> f7b682862 (add versions topic to trinity module) when: task.ext.when == null || task.ext.when @@ -74,4 +70,4 @@ process TRINITY { gzip ${prefix}.fa touch ${prefix}.log """ -} +} \ No newline at end of file From 9d7bbc81c5f8425d7c660aea1fa170aaebcaf0c4 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Tue, 28 Oct 2025 13:53:56 +0000 Subject: [PATCH 4/6] update meta.yml to capture new version topics change --- modules/nf-core/trinity/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trinity/meta.yml b/modules/nf-core/trinity/meta.yml index fe2b7267009a..5af4060881c1 100644 --- a/modules/nf-core/trinity/meta.yml +++ b/modules/nf-core/trinity/meta.yml @@ -77,4 +77,4 @@ authors: - "@gallvp" maintainers: - "@timslittle" - - "@gallvp" + - "@gallvp" \ No newline at end of file From 4bad473dadcabadecbdc260cc534a82f3fe5de6d Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Thu, 4 Dec 2025 16:53:38 +0000 Subject: [PATCH 5/6] update assemblyscan to v1.0.0, allowing json or tsv output --- modules/nf-core/assemblyscan/environment.yml | 2 +- modules/nf-core/assemblyscan/main.nf | 17 ++++++++++------ modules/nf-core/assemblyscan/meta.yml | 14 +++++++++++++ .../assemblyscan/tests/main.nf.test.snap | 20 ++++++++++++++----- 4 files changed, 41 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/assemblyscan/environment.yml b/modules/nf-core/assemblyscan/environment.yml index 47655d685c10..83382a26ab90 100644 --- a/modules/nf-core/assemblyscan/environment.yml +++ b/modules/nf-core/assemblyscan/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::assembly-scan=0.4.1 + - bioconda::assembly-scan=1.0.0 diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 928f792801cc..708c0a30a2e8 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -4,23 +4,28 @@ process ASSEMBLYSCAN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : - 'biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/assembly-scan:1.0.0--pyhdfd78af_0' : + 'biocontainers/assembly-scan:1.0.0--pyhdfd78af_0' }" input: tuple val(meta), path(assembly) output: - tuple val(meta), path("*.json"), emit: json - path "versions.yml" , emit: versions + tuple val(meta), path("*.tsv"), emit: tsv, optional: true + tuple val(meta), path("*.json"), emit: json, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def file_format = (task.ext.args?.contains("--json")) ? "json" : "tsv" """ - assembly-scan ${assembly} > ${prefix}.json + assembly-scan \\ + ${args} \\ + ${assembly} > ${prefix}.${file_format} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/assemblyscan/meta.yml b/modules/nf-core/assemblyscan/meta.yml index d11ea5e9f153..2cfcb78a67cd 100644 --- a/modules/nf-core/assemblyscan/meta.yml +++ b/modules/nf-core/assemblyscan/meta.yml @@ -25,6 +25,18 @@ input: pattern: "*.fasta" ontologies: [] output: + tsv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Assembly statistics in tsv format + pattern: "*.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV json: - - meta: type: map @@ -47,6 +59,8 @@ output: authors: - "@sateeshperi" - "@mjcipriano" + - "@eit-maxlcummins" maintainers: - "@sateeshperi" - "@mjcipriano" + - "@eit-maxlcummins" diff --git a/modules/nf-core/assemblyscan/tests/main.nf.test.snap b/modules/nf-core/assemblyscan/tests/main.nf.test.snap index 3985ac63bbf0..c371897142f5 100644 --- a/modules/nf-core/assemblyscan/tests/main.nf.test.snap +++ b/modules/nf-core/assemblyscan/tests/main.nf.test.snap @@ -8,26 +8,36 @@ "id": "test", "single_end": false }, - "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd" + "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6" ] ], "1": [ - "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21" + + ], + "2": [ + "versions.yml:md5,4113de9fcbbd8f6fc66a5abc7720aa62" ], "json": [ + + ], + "tsv": [ [ { "id": "test", "single_end": false }, - "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd" + "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6" ] ], "versions": [ - "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21" + "versions.yml:md5,4113de9fcbbd8f6fc66a5abc7720aa62" ] } ], - "timestamp": "2023-10-18T15:04:38.644743625" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-12-04T16:48:44.200207939" } } \ No newline at end of file From 1cd9ffb53c3899fc573decb15bbdc4689363109f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 15 Dec 2025 13:39:27 +0000 Subject: [PATCH 6/6] [automated] Fix linting with Prettier --- modules/nf-core/trinity/main.nf | 2 +- modules/nf-core/trinity/meta.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/trinity/main.nf b/modules/nf-core/trinity/main.nf index 78e741f5d84d..3ac485867eee 100644 --- a/modules/nf-core/trinity/main.nf +++ b/modules/nf-core/trinity/main.nf @@ -70,4 +70,4 @@ process TRINITY { gzip ${prefix}.fa touch ${prefix}.log """ -} \ No newline at end of file +} diff --git a/modules/nf-core/trinity/meta.yml b/modules/nf-core/trinity/meta.yml index 5af4060881c1..fe2b7267009a 100644 --- a/modules/nf-core/trinity/meta.yml +++ b/modules/nf-core/trinity/meta.yml @@ -77,4 +77,4 @@ authors: - "@gallvp" maintainers: - "@timslittle" - - "@gallvp" \ No newline at end of file + - "@gallvp"