From f7f63316cc2fc7c99c7975ba4ba64ec1331c2ebe Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 22 Feb 2024 20:05:27 +0000 Subject: [PATCH] Add proper changelog updates --- CHANGELOG.md | 2 +- modules.json | 44 ++----------------- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/cat/fastq/main.nf | 1 - .../umicollapse/tests/main.nf.test.snap | 24 ++++++++-- .../nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/extract/main.nf | 4 +- .../umitools/extract/tests/main.nf.test.snap | 8 +++- 8 files changed, 34 insertions(+), 53 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa3194ac..33f55609 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,7 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `seqkit` | 2.3.1 | 2.6.1 | | `fastqc` | 0.11.4 | 0.12.1 | | `samtools` | 1.17 | 1.19.2 | -| `umitools` | | 1.1.4 | +| `umitools` | | 1.1.5 | | `umicollapse` | | 1.0.0 | ## [v2.2.4](https://github.com/nf-core/smrnaseq/releases/tag/2.2.4) - 2023-11-03 diff --git a/modules.json b/modules.json index ce269067..9bcc37e7 100644 --- a/modules.json +++ b/modules.json @@ -12,12 +12,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882", - "installed_by": ["modules"] - }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", + "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca", "installed_by": ["modules"] }, "fastp": { @@ -62,12 +57,12 @@ }, "umicollapse": { "branch": "master", - "git_sha": "2e561f4551ce3df2bc60016f7ea359f2ed4bce49", + "git_sha": "ba3f3df395d2719dcef5c67189042a1dc555c701", "installed_by": ["modules"] }, "umitools/extract": { "branch": "master", - "git_sha": "9e56d7a647fbf6f7e45ef123bc916ad66b6f7c9d", + "git_sha": "ff7e93715a2acecf3f143ec78c9858deba2984d0", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "untarfiles": { @@ -79,44 +74,11 @@ }, "subworkflows": { "nf-core": { - "bam_sort_stats_samtools": { - "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["subworkflows"] - }, - "bam_stats_samtools": { - "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools", "subworkflows"] - }, "fastq_fastqc_umitools_fastp": { "branch": "master", "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56", "installed_by": ["subworkflows"] - } - } - }, - "subworkflows": { - "nf-core": { - "utils_nextflow_pipeline": { - "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", - "installed_by": ["subworkflows"] - }, - "utils_nfcore_pipeline": { - "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", - "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { - "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", - "installed_by": ["subworkflows"] - } - } - }, - "subworkflows": { - "nf-core": { "utils_nextflow_pipeline": { "branch": "master", "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index bff93add..8c69b121 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 3d963784..f132b2ad 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -76,5 +76,4 @@ process CAT_FASTQ { """ } } - } diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap index 900ff08f..23916f0b 100644 --- a/modules/nf-core/umicollapse/tests/main.nf.test.snap +++ b/modules/nf-core/umicollapse/tests/main.nf.test.snap @@ -7,14 +7,18 @@ "id": "test", "single_end": true }, - "test.dedup.bam:md5,4e86d60aa82242889ab5f9031418ab2e" + "test.dedup.bam:md5,05c5331185263cbee6f508c0669be864" ] ], [ "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" ] ], - "timestamp": "2024-01-30T10:45:28.352669757" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:24:31.850566925" }, "umicollapse fastq tests": { "content": [ @@ -31,6 +35,10 @@ "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, "timestamp": "2024-01-30T10:45:56.053352008" }, "umicollapse stub tests": { @@ -86,6 +94,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, "timestamp": "2024-01-30T10:46:12.482697713" }, "umicollapse paired tests": { @@ -96,13 +108,17 @@ "id": "test", "single_end": false }, - "test.dedup.bam:md5,54be836ec246073e60212445b4369a91" + "test.dedup.bam:md5,f4f05467cb456309fe22851d8b4d4387" ] ], [ "versions.yml:md5,c1e0275d81b1c97a9344d216f9154996" ] ], - "timestamp": "2024-01-30T10:45:44.961261065" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:24:44.166029769" } } \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index 7d08ac0e..aab452d1 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.4 + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 4bd79e79..8719e5f6 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -5,8 +5,8 @@ process UMITOOLS_EXTRACT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' : - 'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }" + 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.5--py39hf95cd2a_0' : + 'biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test.snap b/modules/nf-core/umitools/extract/tests/main.nf.test.snap index 6d5944f1..bf82701d 100644 --- a/modules/nf-core/umitools/extract/tests/main.nf.test.snap +++ b/modules/nf-core/umitools/extract/tests/main.nf.test.snap @@ -2,9 +2,13 @@ "versions": { "content": [ [ - "versions.yml:md5,5a18da2d3a5a4de15e7aaae9082d7abb" + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" ] ], - "timestamp": "2023-12-08T09:41:43.540658352" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T10:01:33.326046137" } } \ No newline at end of file