From a6e310e4ecf3e6f215521f4c2ee83fe8d51d4869 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Fri, 18 Oct 2024 15:54:41 +0200 Subject: [PATCH 1/2] Bump Version of UMICollapse to 1.1.0 --- modules/nf-core/umicollapse/environment.yml | 2 +- modules/nf-core/umicollapse/main.nf | 6 +++--- modules/nf-core/umicollapse/meta.yml | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/umicollapse/environment.yml b/modules/nf-core/umicollapse/environment.yml index 3847980dde4..066f55eef72 100644 --- a/modules/nf-core/umicollapse/environment.yml +++ b/modules/nf-core/umicollapse/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umicollapse=1.0.0 + - bioconda::umicollapse=1.1.0 diff --git a/modules/nf-core/umicollapse/main.nf b/modules/nf-core/umicollapse/main.nf index dae290e6e7a..aec10e85194 100644 --- a/modules/nf-core/umicollapse/main.nf +++ b/modules/nf-core/umicollapse/main.nf @@ -5,8 +5,8 @@ process UMICOLLAPSE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/umicollapse:1.0.0--hdfd78af_1' : - 'biocontainers/umicollapse:1.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/umicollapse:1.1.0--hdfd78af_0' : + 'biocontainers/umicollapse:1.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(bai) @@ -24,7 +24,7 @@ process UMICOLLAPSE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.0.0-1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.1.0-0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. // Memory allocation: We need to make sure that both heap and stack size is sufficiently large for // umicollapse. We set the stack size to 5% of the available memory, the heap size to 90% // which leaves 5% for stuff happening outside of java without the scheduler killing the process. diff --git a/modules/nf-core/umicollapse/meta.yml b/modules/nf-core/umicollapse/meta.yml index 8b366c24438..7c4ebc5ec27 100644 --- a/modules/nf-core/umicollapse/meta.yml +++ b/modules/nf-core/umicollapse/meta.yml @@ -11,7 +11,7 @@ tools: (UMIs)/Random Molecular Tags (RMTs)." homepage: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" documentation: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" - tool_dev_url: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" + tool_dev_url: "https://github.com/siddharthab/UMICollapse" doi: "10.7717/peerj.8275" licence: ["MIT"] identifier: "" @@ -78,4 +78,5 @@ maintainers: - "@CharlotteAnne" - "@chris-cheshire" - "@apeltzer" + - "@siddharthab" - "@MatthiasZepper" From 92f4759d1986853dea5dfd0f82e4de6beed68884 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Tue, 22 Oct 2024 10:49:22 +0000 Subject: [PATCH 2/2] Update test snapshots for umicollapse. --- .../umicollapse/tests/main.nf.test.snap | 24 +++++++++---------- .../tests/main.nf.test.snap | 4 ++-- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap index 3f393eac1ad..bf6d5f30cb4 100644 --- a/modules/nf-core/umicollapse/tests/main.nf.test.snap +++ b/modules/nf-core/umicollapse/tests/main.nf.test.snap @@ -11,14 +11,14 @@ ] ], [ - "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" + "versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-20T08:47:11.402203361" + "timestamp": "2024-10-22T10:43:04.890267074" }, "umicollapse fastq tests": { "content": [ @@ -32,14 +32,14 @@ ] ], [ - "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" + "versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-30T10:45:56.053352008" + "timestamp": "2024-10-22T10:43:45.691571914" }, "umicollapse stub tests": { "content": [ @@ -112,13 +112,13 @@ ] ], [ - "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" + "versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-20T08:47:30.028323337" + "timestamp": "2024-10-22T10:43:33.250587075" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap index ccb96576367..f2b1fb20d9a 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap @@ -49,7 +49,7 @@ [ "versions.yml:md5,20605eb79c410c0ed179ba660d82f75b", "versions.yml:md5,23617661d2c899996bee2b05db027e25", - "versions.yml:md5,268e43f34038d4c6146ed050630f95b4", + "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7", "versions.yml:md5,e02a62a393a833778e16542eeed0d148", "versions.yml:md5,ef00762e264b99ac45713dc0dedf4060" ] @@ -58,7 +58,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:04:02.126366857" + "timestamp": "2024-10-22T10:44:38.266860983" }, "test_bam_dedup_stats_samtools_umicollapse_idxstats": { "content": [