From ba3f3df395d2719dcef5c67189042a1dc555c701 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:59:43 +0100 Subject: [PATCH] Updating samtools in bwamem (#4943) * Updating mulled-container and environment.yml to samtools v1.19.2. Fixing htslib to v1.19.1 * Pinning version of htslib in environment.yml for samblaster * Pinning version of htslib in environment.yml for svdb/merge * Updating snapShot for bwa/mem * Updating snapShot for umicollapse --- modules/nf-core/bwa/mem/environment.yml | 4 +- modules/nf-core/bwa/mem/main.nf | 4 +- .../nf-core/bwa/mem/tests/main.nf.test.snap | 56 ++++++++++++------- modules/nf-core/samblaster/environment.yml | 1 + modules/nf-core/svdb/merge/environment.yml | 1 + .../umicollapse/tests/main.nf.test.snap | 12 ++-- 6 files changed, 48 insertions(+), 30 deletions(-) diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 1818cea3ffa..3f136d0a3fd 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -6,5 +6,5 @@ channels: dependencies: - bwa=0.7.17 # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.18 - - htslib=1.18 + - samtools=1.19.2 + - htslib=1.19.1 diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index a3a8299439a..54ec0f163bf 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -4,8 +4,8 @@ process BWA_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' : - 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:a34558545ae1413d94bde4578787ebef08027945-0' : + 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:a34558545ae1413d94bde4578787ebef08027945-0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap index bfb55fc7e66..e4fd8cc0508 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": true }, - "test.bam:md5,df203d7c7e8fef351408a909570c7952" + "test.bam:md5,a74710a0345b4717bb4431bf9c257120" ] ], "1": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ], "bam": [ [ @@ -20,15 +20,19 @@ "id": "test", "single_end": true }, - "test.bam:md5,df203d7c7e8fef351408a909570c7952" + "test.bam:md5,a74710a0345b4717bb4431bf9c257120" ] ], "versions": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ] } ], - "timestamp": "2023-12-04T11:01:22.483594641" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:11:48.440661587" }, "Single-End Sort": { "content": [ @@ -39,11 +43,11 @@ "id": "test", "single_end": true }, - "test.bam:md5,8a52bd78fdcecb994c1f63897d5b431c" + "test.bam:md5,cb1e038bc4d990683fa485d632550b54" ] ], "1": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ], "bam": [ [ @@ -51,15 +55,19 @@ "id": "test", "single_end": true }, - "test.bam:md5,8a52bd78fdcecb994c1f63897d5b431c" + "test.bam:md5,cb1e038bc4d990683fa485d632550b54" ] ], "versions": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ] } ], - "timestamp": "2023-12-04T11:01:30.180783483" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:11:56.086493265" }, "Paired-End": { "content": [ @@ -70,11 +78,11 @@ "id": "test", "single_end": false }, - "test.bam:md5,9815aef9ec763a60c53c3879be2d73ae" + "test.bam:md5,aea123a3828a99da1906126355f15a12" ] ], "1": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ], "bam": [ [ @@ -82,15 +90,19 @@ "id": "test", "single_end": false }, - "test.bam:md5,9815aef9ec763a60c53c3879be2d73ae" + "test.bam:md5,aea123a3828a99da1906126355f15a12" ] ], "versions": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ] } ], - "timestamp": "2023-12-04T11:01:38.761983007" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:12:03.474974773" }, "Paired-End Sort": { "content": [ @@ -101,11 +113,11 @@ "id": "test", "single_end": false }, - "test.bam:md5,0f0cda73704c4f7ba08af482edcbbe88" + "test.bam:md5,4682087bcdc3617384b375093fecd8dd" ] ], "1": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ], "bam": [ [ @@ -113,14 +125,18 @@ "id": "test", "single_end": false }, - "test.bam:md5,0f0cda73704c4f7ba08af482edcbbe88" + "test.bam:md5,4682087bcdc3617384b375093fecd8dd" ] ], "versions": [ - "versions.yml:md5,a18ac8ef8cfcc7b2cc262c49d4c064f9" + "versions.yml:md5,c32f719a68bb2966c8511d808154d42d" ] } ], - "timestamp": "2023-12-04T11:01:46.284587802" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-19T11:12:10.721510817" } } \ No newline at end of file diff --git a/modules/nf-core/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml index f9bd0f24b98..a6e3038a195 100644 --- a/modules/nf-core/samblaster/environment.yml +++ b/modules/nf-core/samblaster/environment.yml @@ -6,3 +6,4 @@ channels: dependencies: - bioconda::samblaster=0.1.26 - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index 9698a43e5f4..e6fec088773 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -7,3 +7,4 @@ dependencies: - svdb=2.8.1 # renovate: datasource=conda depName=bioconda/samtools - samtools=1.19.2 + - htslib=1.19.1 diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap index 6bbe1603a51..23916f0b976 100644 --- a/modules/nf-core/umicollapse/tests/main.nf.test.snap +++ b/modules/nf-core/umicollapse/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "test", "single_end": true }, - "test.dedup.bam:md5,4e86d60aa82242889ab5f9031418ab2e" + "test.dedup.bam:md5,05c5331185263cbee6f508c0669be864" ] ], [ @@ -16,9 +16,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.01.0" }, - "timestamp": "2024-01-30T10:45:28.352669757" + "timestamp": "2024-02-19T11:24:31.850566925" }, "umicollapse fastq tests": { "content": [ @@ -108,7 +108,7 @@ "id": "test", "single_end": false }, - "test.dedup.bam:md5,54be836ec246073e60212445b4369a91" + "test.dedup.bam:md5,f4f05467cb456309fe22851d8b4d4387" ] ], [ @@ -117,8 +117,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.01.0" }, - "timestamp": "2024-01-30T10:45:44.961261065" + "timestamp": "2024-02-19T11:24:44.166029769" } } \ No newline at end of file