From 2549bc3d5410ea12ea3ff457a467865b2f764c8e Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Tue, 28 Oct 2025 15:27:26 +0100 Subject: [PATCH 01/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 5 +- modules/nf-core/trimgalore/tests/main.nf.test | 10 +- .../trimgalore/tests/main.nf.test.snap | 134 ++++++++++-------- 3 files changed, 81 insertions(+), 68 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 5fe53669f766..cd664eb77806 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//'"), topic: versions, emit: versions_trim_galore when: task.ext.when == null || task.ext.when @@ -55,7 +55,6 @@ process TRIMGALORE { cat <<-END_VERSIONS > versions.yml "${task.process}": - trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS @@ -75,7 +74,6 @@ process TRIMGALORE { cat <<-END_VERSIONS > versions.yml "${task.process}": - trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS @@ -99,7 +97,6 @@ process TRIMGALORE { cat <<-END_VERSIONS > versions.yml "${task.process}": - trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index c01672c49b9e..1123ae96efce 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) } } }, - { assert snapshot(path(process.out.versions.get(0)).yaml).match() }, + { assert snapshot(process.out.versions_trim_galore).match() }, ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out, - path(process.out.versions.get(0)).yaml + process.out.versions_trim_galore ).match() }, ) } @@ -121,7 +121,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) } } }, - { assert snapshot(path(process.out.versions.get(0)).yaml).match() }, + { assert snapshot(process.out.versions_trim_galore).match() }, ) } } @@ -152,7 +152,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.versions.get(0)).yaml, + process.out.versions_trim_galore, process.out.reads, process.out.unpaired ).match() }, @@ -181,7 +181,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() }, - { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }, + { assert snapshot(process.out.versions_trim_galore).match("versions") }, ) } } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index c454ad521f63..268e8362a1c9 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -1,19 +1,19 @@ { "test_trimgalore_single_end": { "content": [ - { - "TRIMGALORE": { - "trimgalore": "0.6.10", - "cutadapt": 4.9, - "pigz": 2.8 - } - } + [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:25:01.330769598" + "timestamp": "2025-10-28T15:17:27.834356" }, "test_trimgalore_single_end - stub": { "content": [ @@ -46,7 +46,11 @@ ], "5": [ - "versions.yml:md5,5928323d579768de37e83c56c821757f" + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] ], "html": [ @@ -72,26 +76,30 @@ "unpaired": [ ], - "versions": [ - "versions.yml:md5,5928323d579768de37e83c56c821757f" + "versions_trim_galore": [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] ], "zip": [ ] }, - { - "TRIMGALORE": { - "trimgalore": "0.6.10", - "cutadapt": 4.9, - "pigz": 2.8 - } - } + [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:25:15.582246999" + "timestamp": "2025-10-28T15:18:48.603599" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -130,7 +138,11 @@ ], "5": [ - "versions.yml:md5,5928323d579768de37e83c56c821757f" + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] ], "html": [ @@ -162,8 +174,12 @@ "unpaired": [ ], - "versions": [ - "versions.yml:md5,5928323d579768de37e83c56c821757f" + "versions_trim_galore": [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] ], "zip": [ @@ -171,52 +187,52 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:26:05.201562315" + "timestamp": "2025-10-28T15:22:52.625834" }, "versions": { "content": [ - { - "TRIMGALORE": { - "trimgalore": "0.6.10", - "cutadapt": 4.9, - "pigz": 2.8 - } - } + [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:26:05.229598492" + "timestamp": "2025-10-28T15:22:52.680293" }, "test_trimgalore_paired_end": { "content": [ - { - "TRIMGALORE": { - "trimgalore": "0.6.10", - "cutadapt": 4.9, - "pigz": 2.8 - } - } + [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:25:33.510924538" + "timestamp": "2025-10-28T15:20:12.004916" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ - { - "TRIMGALORE": { - "trimgalore": "0.6.10", - "cutadapt": 4.9, - "pigz": 2.8 - } - }, + [ + [ + "TRIMGALORE", + "trim_galore", + "wtmp begins To 28 Mar 2024 10:11:54 CET" + ] + ], [ [ { @@ -243,9 +259,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-01-06T12:25:46.461002981" + "timestamp": "2025-10-28T15:21:32.456884" } } \ No newline at end of file From 4a591278678489956b68c11daf035fd0d86ac929 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Tue, 28 Oct 2025 16:30:56 +0100 Subject: [PATCH 02/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 2 +- modules/nf-core/trimgalore/tests/main.nf.test | 3 +-- .../nf-core/trimgalore/tests/main.nf.test.snap | 17 +++++------------ 3 files changed, 7 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index cd664eb77806..ffcd593ddfab 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true - tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//'"), topic: versions, emit: versions_trim_galore + tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>&1) | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/'"), topic: versions, emit: versions_trim_galore when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 1123ae96efce..780bca4c24a9 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -62,8 +62,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out, - process.out.versions_trim_galore + process.out ).match() }, ) } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 268e8362a1c9..25384775cff8 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:17:27.834356" + "timestamp": "2025-10-28T16:23:38.035007" }, "test_trimgalore_single_end - stub": { "content": [ @@ -86,20 +86,13 @@ "zip": [ ] - }, - [ - [ - "TRIMGALORE", - "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" - ] - ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:18:48.603599" + "timestamp": "2025-10-28T16:25:02.342729" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -222,7 +215,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:20:12.004916" + "timestamp": "2025-10-28T16:26:30.256899" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ @@ -262,6 +255,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:21:32.456884" + "timestamp": "2025-10-28T16:27:54.622542" } } \ No newline at end of file From 361d41cb895ada2ea5aafb480d3d07dc0494daf3 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Tue, 28 Oct 2025 23:53:02 +0100 Subject: [PATCH 03/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 14 +---- .../trimgalore/tests/main.nf.test.snap | 60 ++++++++++++++++++- 2 files changed, 60 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index ffcd593ddfab..a07efcc8e68c 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -17,6 +17,8 @@ process TRIMGALORE { tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>&1) | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/'"), topic: versions, emit: versions_trim_galore + tuple val("${task.process}"), val('cutadapt'), eval("echo \$(cutadapt --version 2>&1)"), topic: versions, emit: versions_cutadapt + tuple val("${task.process}"), val('pigz'), eval("echo \$( pigz --version 2>&1 | sed 's/pigz //g' )"), topic: versions, emit: versions_pigz when: task.ext.when == null || task.ext.when @@ -71,12 +73,6 @@ process TRIMGALORE { --gzip \\ ${prefix}_1.fastq.gz \\ ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cutadapt: \$(cutadapt --version) - pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) - END_VERSIONS """ } @@ -94,11 +90,5 @@ process TRIMGALORE { } """ ${output_command} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cutadapt: \$(cutadapt --version) - pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) - END_VERSIONS """ } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 25384775cff8..0ce5c65557e8 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -52,6 +52,20 @@ "wtmp begins To 28 Mar 2024 10:11:54 CET" ] ], + "6": [ + [ + "TRIMGALORE", + "cutadapt", + "4.9" + ] + ], + "7": [ + [ + "TRIMGALORE", + "pigz", + "2.8" + ] + ], "html": [ ], @@ -75,6 +89,20 @@ ], "unpaired": [ + ], + "versions_cutadapt": [ + [ + "TRIMGALORE", + "cutadapt", + "4.9" + ] + ], + "versions_pigz": [ + [ + "TRIMGALORE", + "pigz", + "2.8" + ] ], "versions_trim_galore": [ [ @@ -92,7 +120,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T16:25:02.342729" + "timestamp": "2025-10-28T23:46:03.149552" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -137,6 +165,20 @@ "wtmp begins To 28 Mar 2024 10:11:54 CET" ] ], + "6": [ + [ + "TRIMGALORE", + "cutadapt", + "4.9" + ] + ], + "7": [ + [ + "TRIMGALORE", + "pigz", + "2.8" + ] + ], "html": [ ], @@ -166,6 +208,20 @@ ], "unpaired": [ + ], + "versions_cutadapt": [ + [ + "TRIMGALORE", + "cutadapt", + "4.9" + ] + ], + "versions_pigz": [ + [ + "TRIMGALORE", + "pigz", + "2.8" + ] ], "versions_trim_galore": [ [ @@ -183,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:22:52.625834" + "timestamp": "2025-10-28T23:50:33.818506" }, "versions": { "content": [ From 5575e56dae0ead8c2406d894e6e0d56dcc953b05 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 01:34:17 +0100 Subject: [PATCH 04/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 6 ---- modules/nf-core/trimgalore/tests/main.nf.test | 3 +- .../trimgalore/tests/main.nf.test.snap | 28 +++++++++---------- .../nf-core/trimgalore/tests/nextflow.config | 2 ++ 4 files changed, 17 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index a07efcc8e68c..d32d2790ac47 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -54,12 +54,6 @@ process TRIMGALORE { --cores ${cores} \\ --gzip \\ ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cutadapt: \$(cutadapt --version) - pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) - END_VERSIONS """ } else { diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 780bca4c24a9..dd405a9462c9 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -179,8 +179,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions_trim_galore).match("versions") }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 0ce5c65557e8..9a2a3ec829eb 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -5,7 +5,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ] ], @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T16:23:38.035007" + "timestamp": "2025-10-29T00:44:57.075051" }, "test_trimgalore_single_end - stub": { "content": [ @@ -49,7 +49,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ], "6": [ @@ -108,7 +108,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ], "zip": [ @@ -120,7 +120,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T23:46:03.149552" + "timestamp": "2025-10-29T00:45:14.633846" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -162,7 +162,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ], "6": [ @@ -227,7 +227,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ], "zip": [ @@ -239,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T23:50:33.818506" + "timestamp": "2025-10-29T00:46:21.293799" }, "versions": { "content": [ @@ -247,7 +247,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ] ], @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T15:22:52.680293" + "timestamp": "2025-10-29T00:46:21.34624" }, "test_trimgalore_paired_end": { "content": [ @@ -263,7 +263,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ] ], @@ -271,7 +271,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T16:26:30.256899" + "timestamp": "2025-10-29T00:45:37.475161" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ @@ -279,7 +279,7 @@ [ "TRIMGALORE", "trim_galore", - "wtmp begins To 28 Mar 2024 10:11:54 CET" + "" ] ], [ @@ -311,6 +311,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-28T16:27:54.622542" + "timestamp": "2025-10-29T00:55:01.295113" } } \ No newline at end of file diff --git a/modules/nf-core/trimgalore/tests/nextflow.config b/modules/nf-core/trimgalore/tests/nextflow.config index d8e3ac13790c..4c974dcf37da 100644 --- a/modules/nf-core/trimgalore/tests/nextflow.config +++ b/modules/nf-core/trimgalore/tests/nextflow.config @@ -1,5 +1,7 @@ process { + withName: TRIMGALORE { ext.args = params.module_args } + } From f513c0dffb6d32fa27fd7f3f4e3f80fa58cdb35e Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 01:48:26 +0100 Subject: [PATCH 05/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index d32d2790ac47..1a99a6026418 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true - tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>&1) | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/'"), topic: versions, emit: versions_trim_galore + tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>/dev/null) | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/' || echo 'not found'"), topic: versions, emit: versions_trim_galore tuple val("${task.process}"), val('cutadapt'), eval("echo \$(cutadapt --version 2>&1)"), topic: versions, emit: versions_cutadapt tuple val("${task.process}"), val('pigz'), eval("echo \$( pigz --version 2>&1 | sed 's/pigz //g' )"), topic: versions, emit: versions_pigz From 016fcf13919909b98874c8c0aaef1baa4dc3b545 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 02:05:03 +0100 Subject: [PATCH 06/30] trim_galore version --- modules/nf-core/trimgalore/tests/main.nf.test | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index dd405a9462c9..31ea61cacaad 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -179,7 +179,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match() }, + { assert snapshot(process.out.versions_trim_galore).match("versions") } ) } } From 931053a3bf10243c9b5a4452de11127287316cdd Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 10:32:48 +0100 Subject: [PATCH 07/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 2 +- .../trimgalore/tests/main.nf.test.snap | 28 +++++++++---------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 1a99a6026418..add4595f60b0 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true - tuple val("${task.process}"), val('trim_galore'), eval("echo \$(trim_galore --version 2>/dev/null) | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/' || echo 'not found'"), topic: versions, emit: versions_trim_galore + tuple val("${task.process}"), val('trim_galore'), eval("trim_galore --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/'"), topic: versions, emit: versions_trim_galore tuple val("${task.process}"), val('cutadapt'), eval("echo \$(cutadapt --version 2>&1)"), topic: versions, emit: versions_cutadapt tuple val("${task.process}"), val('pigz'), eval("echo \$( pigz --version 2>&1 | sed 's/pigz //g' )"), topic: versions, emit: versions_pigz diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 9a2a3ec829eb..19d569966951 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -5,7 +5,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ] ], @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:44:57.075051" + "timestamp": "2025-10-29T10:31:14.087754" }, "test_trimgalore_single_end - stub": { "content": [ @@ -49,7 +49,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ], "6": [ @@ -108,7 +108,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ], "zip": [ @@ -120,7 +120,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:45:14.633846" + "timestamp": "2025-10-29T10:31:28.042719" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -162,7 +162,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ], "6": [ @@ -227,7 +227,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ], "zip": [ @@ -239,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:46:21.293799" + "timestamp": "2025-10-29T10:32:16.50115" }, "versions": { "content": [ @@ -247,7 +247,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ] ], @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:46:21.34624" + "timestamp": "2025-10-29T10:32:16.562393" }, "test_trimgalore_paired_end": { "content": [ @@ -263,7 +263,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ] ], @@ -271,7 +271,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:45:37.475161" + "timestamp": "2025-10-29T10:31:44.816057" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ @@ -279,7 +279,7 @@ [ "TRIMGALORE", "trim_galore", - "" + " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" ] ], [ @@ -311,6 +311,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T00:55:01.295113" + "timestamp": "2025-10-29T10:32:00.051031" } } \ No newline at end of file From c99f5df1f0e042192f47365a465d5e3530ccaf91 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 11:06:44 +0100 Subject: [PATCH 08/30] trim_galore version --- modules/nf-core/trimgalore/main.nf | 2 +- .../trimgalore/tests/main.nf.test.snap | 28 +++++++++---------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index add4595f60b0..d974f7b1dc08 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired{,_1,_2}.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html, optional: true tuple val(meta), path("*.zip") , emit: zip, optional: true - tuple val("${task.process}"), val('trim_galore'), eval("trim_galore --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/'"), topic: versions, emit: versions_trim_galore + tuple val("${task.process}"), val('trim_galore'), eval("trim_galore --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+'"), topic: versions, emit: versions_trim_galore tuple val("${task.process}"), val('cutadapt'), eval("echo \$(cutadapt --version 2>&1)"), topic: versions, emit: versions_cutadapt tuple val("${task.process}"), val('pigz'), eval("echo \$( pigz --version 2>&1 | sed 's/pigz //g' )"), topic: versions, emit: versions_pigz diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 19d569966951..91bbb4dd634e 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -5,7 +5,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ] ], @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:31:14.087754" + "timestamp": "2025-10-29T11:05:05.189343" }, "test_trimgalore_single_end - stub": { "content": [ @@ -49,7 +49,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ], "6": [ @@ -108,7 +108,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ], "zip": [ @@ -120,7 +120,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:31:28.042719" + "timestamp": "2025-10-29T11:05:19.966422" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -162,7 +162,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ], "6": [ @@ -227,7 +227,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ], "zip": [ @@ -239,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:32:16.50115" + "timestamp": "2025-10-29T11:06:12.101026" }, "versions": { "content": [ @@ -247,7 +247,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ] ], @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:32:16.562393" + "timestamp": "2025-10-29T11:06:12.163862" }, "test_trimgalore_paired_end": { "content": [ @@ -263,7 +263,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ] ], @@ -271,7 +271,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:31:44.816057" + "timestamp": "2025-10-29T11:05:36.737155" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ @@ -279,7 +279,7 @@ [ "TRIMGALORE", "trim_galore", - " Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n0.6.10\n\n Last update: 02 02 2023" + "0.6.10" ] ], [ @@ -311,6 +311,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T10:32:00.051031" + "timestamp": "2025-10-29T11:05:55.02208" } } \ No newline at end of file From 7b558c1b0c89d49ae7bac9e5d2ca031fb89cfeb7 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 11:43:52 +0100 Subject: [PATCH 09/30] trim_galore version --- modules/nf-core/elprep/filter/meta.yml | 8 ++++++++ modules/nf-core/trimgalore/meta.yml | 11 +++++------ 2 files changed, 13 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml index 51ae6deffeaa..51af18741083 100644 --- a/modules/nf-core/elprep/filter/meta.yml +++ b/modules/nf-core/elprep/filter/meta.yml @@ -115,6 +115,7 @@ output: type: file description: BAM/SAM file pattern: "*.{bam,sam}" + ontologies: [] logs: - - meta: type: map @@ -125,6 +126,7 @@ output: type: file description: Log file pattern: "elprep-*.log" + ontologies: [] metrics: - - meta: type: map @@ -135,6 +137,7 @@ output: type: file description: Metrics file pattern: "*.{metrics.txt}" + ontologies: [] recall: - - meta: type: map @@ -145,6 +148,7 @@ output: type: file description: Recall file pattern: "*.{recall}" + ontologies: [] gvcf: - - meta: type: map @@ -155,6 +159,7 @@ output: type: file description: VCF file pattern: "*.{vcf.gz}" + ontologies: [] table: - - meta: type: map @@ -165,6 +170,7 @@ output: type: file description: Table pattern: "*.{table}" + ontologies: [] activity_profile: - - meta: type: map @@ -175,6 +181,7 @@ output: type: file description: Activity profile pattern: "*.{activity_profile.igv}" + ontologies: [] assembly_regions: - - meta: type: map @@ -185,6 +192,7 @@ output: type: file description: Assembly regions pattern: "*.{assembly_regions.igv}" + ontologies: [] versions: - versions.yml: type: file diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 43ac961cb4e7..a6a83d42912c 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -89,12 +89,11 @@ output: e.g. [ id:'test', single_end:false ] pattern: "*_{fastqc.zip}" versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - versions: + type: file + description: | + File containing software versions used in this module. + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" From 800c313ee9ad354319c5744458fec76a65670ac3 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 12:07:37 +0100 Subject: [PATCH 10/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 18 ++++++++++++------ .../nf-core/trimgalore/tests/main.nf.test.snap | 12 ++++++------ 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index a6a83d42912c..e392b7d8c381 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -88,12 +88,18 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*_{fastqc.zip}" - versions: - - versions: - type: file - description: | - File containing software versions used in this module. - pattern: "versions.yml" + versions_trim_galore: + - - "${task.process}" + - "trim_galore" + - "trim_galore --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+'" + versions_cutadapt: + - - "${task.process}" + - "cutadapt" + - "echo $(cutadapt --version 2>&1)" + versions_pigz: + - - "${task.process}" + - "pigz" + - "echo $(pigz --version 2>&1 | sed 's/pigz //g')" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 91bbb4dd634e..a11829f9e514 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:05:05.189343" + "timestamp": "2025-10-29T12:05:24.301144" }, "test_trimgalore_single_end - stub": { "content": [ @@ -120,7 +120,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:05:19.966422" + "timestamp": "2025-10-29T12:05:37.755723" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -239,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:06:12.101026" + "timestamp": "2025-10-29T12:06:22.93245" }, "versions": { "content": [ @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:06:12.163862" + "timestamp": "2025-10-29T12:06:22.976692" }, "test_trimgalore_paired_end": { "content": [ @@ -271,7 +271,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:05:36.737155" + "timestamp": "2025-10-29T12:05:53.165749" }, "test_trimgalore_paired_end_keep_unpaired": { "content": [ @@ -311,6 +311,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T11:05:55.02208" + "timestamp": "2025-10-29T12:06:09.680104" } } \ No newline at end of file From 50692d05b27bfbe3ef6ad239fe846656ff04062a Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 12:16:07 +0100 Subject: [PATCH 11/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e392b7d8c381..43ac961cb4e7 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -88,18 +88,13 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*_{fastqc.zip}" - versions_trim_galore: - - - "${task.process}" - - "trim_galore" - - "trim_galore --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+'" - versions_cutadapt: - - - "${task.process}" - - "cutadapt" - - "echo $(cutadapt --version 2>&1)" - versions_pigz: - - - "${task.process}" - - "pigz" - - "echo $(pigz --version 2>&1 | sed 's/pigz //g')" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@ewels" From e4ce09ceba4b9af845749bc4d504fffae762d364 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 12:31:17 +0100 Subject: [PATCH 12/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 35 +++++++++++++++++++++++------ 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 43ac961cb4e7..ecd20e505f3c 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -88,13 +88,34 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*_{fastqc.zip}" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_trim_galore: + - - meta: + type: map + description: | + Groovy Map containing sample information + -"versions.yml": + type: map + description: | + Groovy Map containing sample information + + versions_cutadapt: + - - meta: + type: map + description: | + Groovy Map containing sample information + -"versions.yml": + type: map + description: | + Groovy Map containing sample information + versions_pigz: + - - meta: + type: map + description: | + Groovy Map containing sample information + -"versions.yml": + type: map + description: | + Groovy Map containing sample information authors: - "@drpatelh" - "@ewels" From 2a9c652e2c6b4283d6cdb7f431d424eed6d23509 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 12:45:23 +0100 Subject: [PATCH 13/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index ecd20e505f3c..e56def284e55 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -89,30 +89,17 @@ output: e.g. [ id:'test', single_end:false ] pattern: "*_{fastqc.zip}" versions_trim_galore: - - - meta: + - trimgalore: type: map description: | Groovy Map containing sample information - -"versions.yml": - type: map - description: | - Groovy Map containing sample information - versions_cutadapt: - - - meta: - type: map - description: | - Groovy Map containing sample information - -"versions.yml": + - cutadapt: type: map description: | Groovy Map containing sample information versions_pigz: - - - meta: - type: map - description: | - Groovy Map containing sample information - -"versions.yml": + - pigz: type: map description: | Groovy Map containing sample information From 4c1a2e33107e41f0f639b1b99c921162c8ec8254 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 14:31:29 +0100 Subject: [PATCH 14/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 132 ++++++++++------------------ 1 file changed, 47 insertions(+), 85 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e56def284e55..321c46975a54 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -16,93 +16,55 @@ tools: licence: ["GPL-3.0-or-later"] identifier: "" input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - ontologies: [] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + ontologies: [] output: - reads: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*report.txt": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*_{report.txt}" - unpaired: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*unpaired{,_1,_2}.fq.gz": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*unpaired*.fq.gz" - html: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*_{fastqc.html}" - zip: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: map - description: | - Groovy Map containing sample information + - reads: + type: array # Because the main.nf emits a tuple: tuple val(meta), path(reads) + description: Trimmed FastQ file(s). + pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" + # The meta map structure is defined implicitly by the 'type: array' + # matching the tuple val(meta) in main.nf + -log: + type: file # Because the main.nf emits a tuple: tuple val(meta), path(reads) + description: Trimmed FastQ file(s). + pattern: "*_{report.txt}" + # The meta map structure is defined implicitly by the 'type: array' + # matching the tuple val(meta) in main.nf + -unpaired: + type: file + description: | + Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*_{fastqc.zip}" - versions_trim_galore: - - trimgalore: - type: map - description: | - Groovy Map containing sample information - versions_cutadapt: - - cutadapt: - type: map - description: | - Groovy Map containing sample information - versions_pigz: - - pigz: - type: map - description: | - Groovy Map containing sample information + pattern: "*unpaired*.fq.gz" + -html: + type: file + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{fastqc.html}" + -zip: + type: file + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{fastqc.zip}" + - versions_trim_galore: + type: array # Matches the tuple structure in main.nf: [task.process, 'trim_galore', version] + description: Trim Galore! version information. + pattern: "*" # Matches the content of the tuple + - versions_cutadapt: + type: array # Matches the tuple structure in main.nf: [task.process, 'cutadapt', version] + description: Cutadapt version information (Trim Galore! dependency). + pattern: "*" + - versions_pigz: + type: array # Matches the tuple structure in main.nf: [task.process, 'pigz', version] + description: pigz version information (used for parallel compression/decompression). + pattern: "*" authors: - "@drpatelh" - "@ewels" From 8a295774a0e81fe5e8856ebb51698999dce14f06 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 14:42:23 +0100 Subject: [PATCH 15/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 54 ++++++++++++----------------- 1 file changed, 22 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 321c46975a54..9c71fe87ae7c 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -24,47 +24,37 @@ input: ontologies: [] output: - reads: - type: array # Because the main.nf emits a tuple: tuple val(meta), path(reads) + type: array # Matches the tuple val(meta), path(...) in main.nf description: Trimmed FastQ file(s). pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - # The meta map structure is defined implicitly by the 'type: array' - # matching the tuple val(meta) in main.nf - -log: - type: file # Because the main.nf emits a tuple: tuple val(meta), path(reads) - description: Trimmed FastQ file(s). - pattern: "*_{report.txt}" - # The meta map structure is defined implicitly by the 'type: array' - # matching the tuple val(meta) in main.nf - -unpaired: + - log: type: file - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + [cite_start]description: Log file generated by Trim Galore![cite: 2]. + pattern: "*report.txt" + - unpaired: + type: file + [cite_start]description: Unpaired FastQ file(s) generated when processing paired-end data[cite: 2]. pattern: "*unpaired*.fq.gz" - -html: + - html: type: file - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*_{fastqc.html}" - -zip: + [cite_start]description: FastQC report HTML file generated by Trim Galore![cite: 3]. + pattern: "*.html" + - zip: type: file - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*_{fastqc.zip}" + [cite_start]description: FastQC report ZIP file generated by Trim Galore![cite: 3]. + pattern: "*.zip" - versions_trim_galore: - type: array # Matches the tuple structure in main.nf: [task.process, 'trim_galore', version] - description: Trim Galore! version information. - pattern: "*" # Matches the content of the tuple + type: array # Matches the tuple [task.process, 'trim_galore', version] + [cite_start]description: Trim Galore! version information[cite: 4]. + pattern: "*" - versions_cutadapt: - type: array # Matches the tuple structure in main.nf: [task.process, 'cutadapt', version] - description: Cutadapt version information (Trim Galore! dependency). - pattern: "*" + type: array + description: Cutadapt version information (Trim Galore! dependency). + pattern: "*" - versions_pigz: - type: array # Matches the tuple structure in main.nf: [task.process, 'pigz', version] - description: pigz version information (used for parallel compression/decompression). - pattern: "*" + type: array + description: pigz version information (used for parallel compression/decompression). + pattern: "*" authors: - "@drpatelh" - "@ewels" From 978423c5597e7ae8c0a1467aae62f975051dc5cd Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 15:02:00 +0100 Subject: [PATCH 16/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 9c71fe87ae7c..3eb798b7f3aa 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -29,23 +29,23 @@ output: pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: type: file - [cite_start]description: Log file generated by Trim Galore![cite: 2]. + description: Log file generated by Trim Galore!. pattern: "*report.txt" - unpaired: type: file - [cite_start]description: Unpaired FastQ file(s) generated when processing paired-end data[cite: 2]. + description: Unpaired FastQ file(s) generated when processing paired-end data. pattern: "*unpaired*.fq.gz" - html: type: file - [cite_start]description: FastQC report HTML file generated by Trim Galore![cite: 3]. + description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" - zip: type: file - [cite_start]description: FastQC report ZIP file generated by Trim Galore![cite: 3]. + description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" - versions_trim_galore: type: array # Matches the tuple [task.process, 'trim_galore', version] - [cite_start]description: Trim Galore! version information[cite: 4]. + description: Trim Galore! version information. pattern: "*" - versions_cutadapt: type: array From 2ba013d6c30c5b93d818defeed9dd0d4ea9ae59d Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 15:31:48 +0100 Subject: [PATCH 17/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 56 +++++++++---------- .../trimgalore/tests/main.nf.test.snap | 6 +- 2 files changed, 30 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 3eb798b7f3aa..1efbd5582a59 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -17,44 +17,42 @@ tools: identifier: "" input: - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - ontologies: [] + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] output: - reads: - type: array # Matches the tuple val(meta), path(...) in main.nf - description: Trimmed FastQ file(s). - pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" + type: array # Matches the tuple val(meta), path(...) in main.nf + description: Trimmed FastQ file(s). + pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: - type: file - description: Log file generated by Trim Galore!. - pattern: "*report.txt" + type: file + description: Log file generated by Trim Galore!. + pattern: "*report.txt" - unpaired: - type: file - description: Unpaired FastQ file(s) generated when processing paired-end data. - pattern: "*unpaired*.fq.gz" + type: file + description: Unpaired FastQ file(s) generated when processing paired-end data. + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report HTML file generated by Trim Galore!. - pattern: "*.html" + type: file + description: FastQC report HTML file generated by Trim Galore!. + pattern: "*.html" - zip: - type: file - description: FastQC report ZIP file generated by Trim Galore!. - pattern: "*.zip" + type: file + description: FastQC report ZIP file generated by Trim Galore!. + pattern: "*.zip" - versions_trim_galore: - type: array # Matches the tuple [task.process, 'trim_galore', version] - description: Trim Galore! version information. - pattern: "*" + type: array # Matches the tuple [task.process, 'trim_galore', version] + description: Trim Galore! version information. + pattern: "*" - versions_cutadapt: - type: array - description: Cutadapt version information (Trim Galore! dependency). - pattern: "*" + type: array + description: Cutadapt version information (Trim Galore! dependency). + pattern: "*" - versions_pigz: - type: array - description: pigz version information (used for parallel compression/decompression). - pattern: "*" + type: array + description: pigz version information (used for parallel compression/decompression). + pattern: "*" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index a11829f9e514..f4dad84f3cc6 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T12:05:24.301144" + "timestamp": "2025-10-29T15:29:36.5109" }, "test_trimgalore_single_end - stub": { "content": [ @@ -239,7 +239,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T12:06:22.93245" + "timestamp": "2025-10-29T15:28:58.19021" }, "versions": { "content": [ @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-29T12:06:22.976692" + "timestamp": "2025-10-29T15:28:58.254722" }, "test_trimgalore_paired_end": { "content": [ From 6a12b6af4b46b6bcf7fa03b502268238d99c8e62 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 15:38:17 +0100 Subject: [PATCH 18/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 1efbd5582a59..e17d911d1552 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -22,7 +22,7 @@ input: ontologies: [] output: - reads: - type: array # Matches the tuple val(meta), path(...) in main.nf + type: file # Matches the tuple val(meta), path(...) in main.nf description: Trimmed FastQ file(s). pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: @@ -42,15 +42,15 @@ output: description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" - versions_trim_galore: - type: array # Matches the tuple [task.process, 'trim_galore', version] + type: txt # Matches the tuple [task.process, 'trim_galore', version] description: Trim Galore! version information. pattern: "*" - versions_cutadapt: - type: array + type: txt description: Cutadapt version information (Trim Galore! dependency). pattern: "*" - versions_pigz: - type: array + type: txt description: pigz version information (used for parallel compression/decompression). pattern: "*" authors: From 9b9bbe0d5eb31ec62a32ba15765727e5a2019540 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 15:49:16 +0100 Subject: [PATCH 19/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e17d911d1552..38852aa73f27 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -17,12 +17,12 @@ tools: identifier: "" input: - reads: - type: file + type: array description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. ontologies: [] output: - reads: - type: file # Matches the tuple val(meta), path(...) in main.nf + type: array # Matches the tuple val(meta), path(...) in main.nf description: Trimmed FastQ file(s). pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: @@ -42,15 +42,15 @@ output: description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" - versions_trim_galore: - type: txt # Matches the tuple [task.process, 'trim_galore', version] + type: array # Matches the tuple [task.process, 'trim_galore', version] description: Trim Galore! version information. pattern: "*" - versions_cutadapt: - type: txt + type: array description: Cutadapt version information (Trim Galore! dependency). pattern: "*" - versions_pigz: - type: txt + type: array description: pigz version information (used for parallel compression/decompression). pattern: "*" authors: From c7dacfb176230875eafd5d3a40d73f2d9c5624eb Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 16:12:49 +0100 Subject: [PATCH 20/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 54 ++++++++++++++--------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 38852aa73f27..770c3ae95322 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -17,42 +17,42 @@ tools: identifier: "" input: - reads: - type: array - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - ontologies: [] + type: array + description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] output: - reads: - type: array # Matches the tuple val(meta), path(...) in main.nf - description: Trimmed FastQ file(s). - pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" + type: array # Matches the tuple val(meta), path(...) in main.nf + description: Trimmed FastQ file(s). + pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - log: - type: file - description: Log file generated by Trim Galore!. - pattern: "*report.txt" + type: file + description: Log file generated by Trim Galore!. + pattern: "*report.txt" - unpaired: - type: file - description: Unpaired FastQ file(s) generated when processing paired-end data. - pattern: "*unpaired*.fq.gz" + type: file + description: Unpaired FastQ file(s) generated when processing paired-end data. + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report HTML file generated by Trim Galore!. - pattern: "*.html" + type: file + description: FastQC report HTML file generated by Trim Galore!. + pattern: "*.html" - zip: - type: file - description: FastQC report ZIP file generated by Trim Galore!. - pattern: "*.zip" + type: file + description: FastQC report ZIP file generated by Trim Galore!. + pattern: "*.zip" - versions_trim_galore: - type: array # Matches the tuple [task.process, 'trim_galore', version] - description: Trim Galore! version information. - pattern: "*" + type: array # Matches the tuple [task.process, 'trim_galore', version] + description: Trim Galore! version information. + pattern: "*" - versions_cutadapt: - type: array - description: Cutadapt version information (Trim Galore! dependency). - pattern: "*" + type: array + description: Cutadapt version information (Trim Galore! dependency). + pattern: "*" - versions_pigz: - type: array - description: pigz version information (used for parallel compression/decompression). - pattern: "*" + type: array + description: pigz version information (used for parallel compression/decompression). + pattern: "*" authors: - "@drpatelh" - "@ewels" From 816bbf0404245870d64fc5ebd0fb135e6e32feff Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 16:29:03 +0100 Subject: [PATCH 21/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 64 ++++++++++++++--------------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 770c3ae95322..35ca729a0f99 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -21,38 +21,38 @@ input: description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. ontologies: [] output: - - reads: - type: array # Matches the tuple val(meta), path(...) in main.nf - description: Trimmed FastQ file(s). - pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" - - log: - type: file - description: Log file generated by Trim Galore!. - pattern: "*report.txt" - - unpaired: - type: file - description: Unpaired FastQ file(s) generated when processing paired-end data. - pattern: "*unpaired*.fq.gz" - - html: - type: file - description: FastQC report HTML file generated by Trim Galore!. - pattern: "*.html" - - zip: - type: file - description: FastQC report ZIP file generated by Trim Galore!. - pattern: "*.zip" - - versions_trim_galore: - type: array # Matches the tuple [task.process, 'trim_galore', version] - description: Trim Galore! version information. - pattern: "*" - - versions_cutadapt: - type: array - description: Cutadapt version information (Trim Galore! dependency). - pattern: "*" - - versions_pigz: - type: array - description: pigz version information (used for parallel compression/decompression). - pattern: "*" + reads: + type: array # Matches the tuple val(meta), path(...) in main.nf + description: Trimmed FastQ file(s). + pattern: "*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz" + log: + type: file + description: Log file generated by Trim Galore!. + pattern: "*report.txt" + unpaired: + type: file + description: Unpaired FastQ file(s) generated when processing paired-end data. + pattern: "*unpaired*.fq.gz" + html: + type: file + description: FastQC report HTML file generated by Trim Galore!. + pattern: "*.html" + zip: + type: file + description: FastQC report ZIP file generated by Trim Galore!. + pattern: "*.zip" + versions_trim_galore: + type: array # Matches the tuple [task.process, 'trim_galore', version] + description: Trim Galore! version information. + pattern: "*" + versions_cutadapt: + type: array + description: Cutadapt version information (Trim Galore! dependency). + pattern: "*" + versions_pigz: + type: array + description: pigz version information (used for parallel compression/decompression). + pattern: "*" authors: - "@drpatelh" - "@ewels" From 784b59cd5d2a6a66270d013acf4d4c84902e8e3d Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 16:37:43 +0100 Subject: [PATCH 22/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 35ca729a0f99..77a567e268a9 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: file + type: array description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 27ce7273d0b21f2d60984a8f7eba4ed871e480bd Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 16:47:13 +0100 Subject: [PATCH 23/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 77a567e268a9..71f10a951313 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: array + type: file[] description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 424e4c5ba8025af98c1273ae178d6ed6dcdac17c Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 16:55:32 +0100 Subject: [PATCH 24/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 71f10a951313..35ca729a0f99 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: file[] + type: file description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 4c89546a1eecae587ed6053ace3e37fa6c168300 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Wed, 29 Oct 2025 17:08:43 +0100 Subject: [PATCH 25/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 35ca729a0f99..4c6364caf7d9 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: file + type: string description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 0e7d2728ada70e737088d03bcef2b23bb1f96d6f Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Thu, 30 Oct 2025 00:06:26 +0100 Subject: [PATCH 26/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 4c6364caf7d9..77a567e268a9 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: string + type: array description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 4a2ef9df2816b8c2771448ed3e7462bbb2afc52b Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Thu, 30 Oct 2025 00:14:49 +0100 Subject: [PATCH 27/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index 77a567e268a9..e9f8b8c33568 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -39,8 +39,11 @@ output: pattern: "*.html" zip: type: array - description: FastQC report ZIP file generated by Trim Galore!. - pattern: "*.zip" + # Explicitly declare that the items in the array are Files + items: + type: File + description: FastQC report ZIP file generated by Trim Galore!. + pattern: "*.zip" versions_trim_galore: type: array # Matches the tuple [task.process, 'trim_galore', version] description: Trim Galore! version information. From 8e979908c134226d9f1183952a7093c910730b7e Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Mon, 3 Nov 2025 00:06:01 +0200 Subject: [PATCH 28/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e9f8b8c33568..b54b6aefe83b 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,10 +38,9 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: array - # Explicitly declare that the items in the array are Files + type: array # Explicitly declare that the items in the array are Files items: - type: File + type: file description: FastQC report ZIP file generated by Trim Galore!. pattern: "*.zip" versions_trim_galore: From 78bdd5fce09817040e731ac206968f1d53941baf Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Mon, 3 Nov 2025 01:46:13 +0200 Subject: [PATCH 29/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index b54b6aefe83b..d777269d0389 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,7 +38,7 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: array # Explicitly declare that the items in the array are Files + type: file # Explicitly declare that the items in the array are Files items: type: file description: FastQC report ZIP file generated by Trim Galore!. From d19c7b7e7ebf92f81a8ad2d284da809e4d6210f5 Mon Sep 17 00:00:00 2001 From: Bhagwan Yadav Date: Mon, 3 Nov 2025 02:01:42 +0200 Subject: [PATCH 30/30] trim_galore version --- modules/nf-core/trimgalore/meta.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index d777269d0389..3c0fd15edf73 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -38,11 +38,8 @@ output: description: FastQC report HTML file generated by Trim Galore!. pattern: "*.html" zip: - type: file # Explicitly declare that the items in the array are Files - items: - type: file - description: FastQC report ZIP file generated by Trim Galore!. - pattern: "*.zip" + - - meta + - "*.zip" versions_trim_galore: type: array # Matches the tuple [task.process, 'trim_galore', version] description: Trim Galore! version information.