From 070b1ad7a9732b2ddc66fbb1407da05af8ff8ff9 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 16 Jan 2025 07:10:34 -0600 Subject: [PATCH] Update seqkit to version 2.9.0 (#7314) * Update seqkit to version 2.9.0 * Add stub sections where missing * Update nf-test checksums --- modules/nf-core/seqkit/fx2tab/environment.yml | 2 +- modules/nf-core/seqkit/fx2tab/main.nf | 16 +++++- .../seqkit/fx2tab/tests/main.nf.test.snap | 34 ++++++------ modules/nf-core/seqkit/tab2fx/environment.yml | 2 +- modules/nf-core/seqkit/tab2fx/main.nf | 16 +++++- .../seqkit/tab2fx/tests/main.nf.test.snap | 54 +++++++++---------- 6 files changed, 74 insertions(+), 50 deletions(-) diff --git a/modules/nf-core/seqkit/fx2tab/environment.yml b/modules/nf-core/seqkit/fx2tab/environment.yml index 41f3e7de43d..1f93892f485 100644 --- a/modules/nf-core/seqkit/fx2tab/environment.yml +++ b/modules/nf-core/seqkit/fx2tab/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::seqkit=2.8.1 + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/fx2tab/main.nf b/modules/nf-core/seqkit/fx2tab/main.nf index d96b0b9d370..7a3f4103391 100644 --- a/modules/nf-core/seqkit/fx2tab/main.nf +++ b/modules/nf-core/seqkit/fx2tab/main.nf @@ -4,8 +4,8 @@ process SEQKIT_FX2TAB { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' : - 'biocontainers/seqkit:2.8.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' : + 'biocontainers/seqkit:2.9.0--h9ee0642_0' }" input: tuple val(meta), path(fastx) @@ -34,4 +34,16 @@ process SEQKIT_FX2TAB { seqkit: \$( seqkit | sed '3!d; s/Version: //' ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "txt.zst" + """ + touch ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap b/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap index 29421657250..38c0b645ee2 100644 --- a/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap +++ b/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap @@ -7,30 +7,30 @@ { "id": "test" }, - "test.txt.zst:md5,08902131ebe68052a97178bc426bf944" + "test.txt.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ], "text": [ [ { "id": "test" }, - "test.txt.zst:md5,08902131ebe68052a97178bc426bf944" + "test.txt.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-07T16:01:39.484590737" + "timestamp": "2025-01-15T12:18:24.281141" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ], "text": [ [ @@ -55,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-07T16:01:21.332957847" + "timestamp": "2025-01-15T12:18:14.007765" }, "sarscov2 - fastq": { "content": [ @@ -77,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ], "text": [ [ @@ -88,14 +88,14 @@ ] ], "versions": [ - "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8" + "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-07T16:01:29.885155029" + "timestamp": "2025-01-15T12:18:19.228692" } } \ No newline at end of file diff --git a/modules/nf-core/seqkit/tab2fx/environment.yml b/modules/nf-core/seqkit/tab2fx/environment.yml index 41f3e7de43d..1f93892f485 100644 --- a/modules/nf-core/seqkit/tab2fx/environment.yml +++ b/modules/nf-core/seqkit/tab2fx/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::seqkit=2.8.1 + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/tab2fx/main.nf b/modules/nf-core/seqkit/tab2fx/main.nf index 9532cfc5918..9cdee7d30ba 100644 --- a/modules/nf-core/seqkit/tab2fx/main.nf +++ b/modules/nf-core/seqkit/tab2fx/main.nf @@ -4,8 +4,8 @@ process SEQKIT_TAB2FX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' : - 'biocontainers/seqkit:2.8.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' : + 'biocontainers/seqkit:2.9.0--h9ee0642_0' }" input: tuple val(meta), path(text) @@ -34,4 +34,16 @@ process SEQKIT_TAB2FX { seqkit: \$( seqkit | sed '3!d; s/Version: //' ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "fa.zst" + """ + touch ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap b/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap index 857a2b2e953..91c6fbbb5c2 100644 --- a/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap +++ b/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap @@ -7,30 +7,30 @@ { "id": "test" }, - "test.fa.zst:md5,04d45a85c10933605cb5a289552c83a0" + "test.fa.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ], "fastx": [ [ { "id": "test" }, - "test.fa.zst:md5,04d45a85c10933605cb5a289552c83a0" + "test.fa.zst:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-08T08:24:24.025365917" + "timestamp": "2025-01-15T12:20:30.19388" }, "fastq_gz": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ], "fastx": [ [ @@ -55,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-08T08:24:12.779036251" + "timestamp": "2025-01-15T12:20:25.318142" }, "fasta_gz": { "content": [ @@ -77,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ], "fastx": [ [ @@ -88,15 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-08T08:24:00.497912668" + "timestamp": "2025-01-15T12:20:19.111781" }, "fasta": { "content": [ @@ -110,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ], "fastx": [ [ @@ -121,15 +121,15 @@ ] ], "versions": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-08T08:23:31.940090506" + "timestamp": "2025-01-15T12:20:06.405339" }, "fastq": { "content": [ @@ -143,7 +143,7 @@ ] ], "1": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ], "fastx": [ [ @@ -154,14 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36" + "versions.yml:md5,d01878090b875a05b111ee8a68405491" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-05-08T08:23:46.059347765" + "timestamp": "2025-01-15T12:20:12.813847" } } \ No newline at end of file