From 33534b4edd6ea8a623edbcf48179f4017559071d Mon Sep 17 00:00:00 2001 From: Sebastien Guizard Date: Thu, 2 Jul 2026 15:00:03 +0100 Subject: [PATCH 1/4] gstama_polyacleanup: Fixed regression - Revert to original globs --- modules/nf-core/gstama/polyacleanup/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 61b98b076544..b8bd55b031a0 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -11,9 +11,9 @@ process GSTAMA_POLYACLEANUP { tuple val(meta), path(fasta) output: - tuple val(meta), path("*.fa.gz") , emit: fasta - tuple val(meta), path("*_polya_flnc_report.txt.gz"), emit: report - tuple val(meta), path("*_tails.fa.gz") , emit: tails + tuple val(meta), path("*_tama.fa.gz") , emit: fasta + tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report + tuple val(meta), path("*_tama_tails.fa.gz") , emit: tails tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions when: From abfa5d3db3fab4a6159e5c8efe5efa2894f59fa8 Mon Sep 17 00:00:00 2001 From: Sebastien Guizard Date: Thu, 2 Jul 2026 15:13:34 +0100 Subject: [PATCH 2/4] gstama_polyacleanup: Fixed regression - Update meta.yml --- modules/nf-core/gstama/polyacleanup/meta.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index 598c4be6029d..59bb5199c684 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -37,7 +37,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.fa.gz": + - "*_tama.fa.gz": type: file description: The Full Length Non Chimeric reads cleaned from remaining polyA tails. The sequences are in FASTA format compressed with gzip. @@ -50,7 +50,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_polya_flnc_report.txt.gz": + - "*_tama_polya_flnc_report.txt.gz": type: file description: A text file describing the number of polyA tails removed and their length. Compressed with gzip. @@ -63,7 +63,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_tails.fa.gz": + - "*_tama_tails.fa.gz": type: file description: A gzip compressed FASTA file of trimmed polyA tails. pattern: "*_tails.fa.gz" From a046be70fdf785e777be412cc16c59b1d236e0d0 Mon Sep 17 00:00:00 2001 From: Sebastien Guizard Date: Thu, 2 Jul 2026 16:32:54 +0100 Subject: [PATCH 3/4] Update output file names in GSTAMA_POLYACLEANUP process and tests --- modules/nf-core/gstama/polyacleanup/main.nf | 13 ++++++---- modules/nf-core/gstama/polyacleanup/meta.yml | 6 ++--- .../polyacleanup/tests/main.nf.test.snap | 26 +++++++------------ 3 files changed, 21 insertions(+), 24 deletions(-) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index b8bd55b031a0..be37f27adaea 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -11,9 +11,9 @@ process GSTAMA_POLYACLEANUP { tuple val(meta), path(fasta) output: - tuple val(meta), path("*_tama.fa.gz") , emit: fasta - tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report - tuple val(meta), path("*_tama_tails.fa.gz") , emit: tails + tuple val(meta), path("*_seq.fa.gz") , emit: fasta + tuple val(meta), path("*_polya_flnc_report.txt.gz"), emit: report + tuple val(meta), path("*_tails.fa.gz") , emit: tails tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions when: @@ -28,7 +28,10 @@ process GSTAMA_POLYACLEANUP { -f $fasta \\ -p ${prefix} \\ $args - gzip ${prefix}.fa + + mv ${prefix}.fa ${prefix}_seq.fa + + gzip ${prefix}_seq.fa gzip ${prefix}_polya_flnc_report.txt gzip ${prefix}_tails.fa """ @@ -36,7 +39,7 @@ process GSTAMA_POLYACLEANUP { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - echo "" | gzip > ${prefix}.fa.gz + echo "" | gzip > ${prefix}_seq.fa.gz echo "" | gzip > ${prefix}_polya_flnc_report.txt.gz echo "" | gzip > ${prefix}_tails.fa.gz """ diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index 59bb5199c684..ae7d405f2004 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -37,7 +37,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_tama.fa.gz": + - "*_seq.fa.gz": type: file description: The Full Length Non Chimeric reads cleaned from remaining polyA tails. The sequences are in FASTA format compressed with gzip. @@ -50,7 +50,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_tama_polya_flnc_report.txt.gz": + - "*_polya_flnc_report.txt.gz": type: file description: A text file describing the number of polyA tails removed and their length. Compressed with gzip. @@ -63,7 +63,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_tama_tails.fa.gz": + - "*_tails.fa.gz": type: file description: A gzip compressed FASTA file of trimmed polyA tails. pattern: "*_tails.fa.gz" diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap index e2227103f00d..9697a1e202fa 100644 --- a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap @@ -7,10 +7,7 @@ { "id": "test" }, - [ - "test.fa.gz:md5,f0a2c3ca8f19d2197c6b5b273093ebf0", - "test_tails.fa.gz:md5,20a02db3d29cc45b39880e1ad5ee243b" - ] + "test_seq.fa.gz:md5,f0a2c3ca8f19d2197c6b5b273093ebf0" ] ], "report": [ @@ -38,11 +35,11 @@ ] } ], - "timestamp": "2026-05-11T23:18:48.341014322", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.03.2" - } + "nf-test": "0.9.3", + "nextflow": "26.04.4" + }, + "timestamp": "2026-07-02T16:13:41.994675873" }, "test-gstama-polyacleanup -- stub": { "content": [ @@ -52,10 +49,7 @@ { "id": "test" }, - [ - "test.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_tails.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test_seq.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "report": [ @@ -83,10 +77,10 @@ ] } ], - "timestamp": "2026-05-11T23:18:56.653882224", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.03.2" - } + "nf-test": "0.9.3", + "nextflow": "26.04.4" + }, + "timestamp": "2026-07-02T16:13:49.869293504" } } \ No newline at end of file From 071ac453ba84a7d9c8abc326130f8ee745330ec5 Mon Sep 17 00:00:00 2001 From: Sebastien Guizard Date: Fri, 3 Jul 2026 09:01:27 +0100 Subject: [PATCH 4/4] Rename fasta channel to seq --- modules/nf-core/gstama/polyacleanup/main.nf | 2 +- modules/nf-core/gstama/polyacleanup/meta.yml | 2 +- .../polyacleanup/tests/main.nf.test.snap | 20 +++++++++---------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index be37f27adaea..20a33d05b52c 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -11,7 +11,7 @@ process GSTAMA_POLYACLEANUP { tuple val(meta), path(fasta) output: - tuple val(meta), path("*_seq.fa.gz") , emit: fasta + tuple val(meta), path("*_seq.fa.gz") , emit: seq tuple val(meta), path("*_polya_flnc_report.txt.gz"), emit: report tuple val(meta), path("*_tails.fa.gz") , emit: tails tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index ae7d405f2004..76e59bcb5394 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -31,7 +31,7 @@ input: pattern: "*.{fa,fasta}" ontologies: [] output: - fasta: + seq: - - meta: type: map description: | diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap index 9697a1e202fa..5546752c0bb0 100644 --- a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap @@ -2,20 +2,20 @@ "test-gstama-polyacleanup": { "content": [ { - "fasta": [ + "report": [ [ { "id": "test" }, - "test_seq.fa.gz:md5,f0a2c3ca8f19d2197c6b5b273093ebf0" + "test_polya_flnc_report.txt.gz:md5,83ba9d11a59ff516f45dd45c78613206" ] ], - "report": [ + "seq": [ [ { "id": "test" }, - "test_polya_flnc_report.txt.gz:md5,83ba9d11a59ff516f45dd45c78613206" + "test_seq.fa.gz:md5,f0a2c3ca8f19d2197c6b5b273093ebf0" ] ], "tails": [ @@ -39,25 +39,25 @@ "nf-test": "0.9.3", "nextflow": "26.04.4" }, - "timestamp": "2026-07-02T16:13:41.994675873" + "timestamp": "2026-07-03T08:49:26.133692481" }, "test-gstama-polyacleanup -- stub": { "content": [ { - "fasta": [ + "report": [ [ { "id": "test" }, - "test_seq.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_polya_flnc_report.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "report": [ + "seq": [ [ { "id": "test" }, - "test_polya_flnc_report.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_seq.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "tails": [ @@ -81,6 +81,6 @@ "nf-test": "0.9.3", "nextflow": "26.04.4" }, - "timestamp": "2026-07-02T16:13:49.869293504" + "timestamp": "2026-07-03T08:49:31.508481265" } } \ No newline at end of file