From 547d15c4d1a2826a35cf799f507562a9e09b99ff Mon Sep 17 00:00:00 2001 From: Andries van Tonder Date: Mon, 15 Sep 2025 15:14:51 +0100 Subject: [PATCH] pre-release dev --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 16 +- modules.json | 26 ++-- .../nf-core/bcftools/filter/environment.yml | 5 +- modules/nf-core/bcftools/filter/main.nf | 4 +- .../bcftools/filter/tests/main.nf.test.snap | 74 ++++----- .../nf-core/bcftools/filter/tests/tags.yml | 2 - .../nf-core/bcftools/index/environment.yml | 5 +- modules/nf-core/bcftools/index/main.nf | 4 +- .../bcftools/index/tests/main.nf.test.snap | 28 ++-- modules/nf-core/bcftools/index/tests/tags.yml | 2 - .../nf-core/bcftools/query/environment.yml | 5 +- modules/nf-core/bcftools/query/main.nf | 4 +- .../bcftools/query/tests/main.nf.test.snap | 18 +-- modules/nf-core/bcftools/query/tests/tags.yml | 2 - modules/nf-core/bcftools/sort/environment.yml | 5 +- modules/nf-core/bcftools/sort/main.nf | 4 +- .../bcftools/sort/tests/main.nf.test.snap | 58 +++---- modules/nf-core/bcftools/sort/tests/tags.yml | 2 - .../nf-core/bcftools/stats/environment.yml | 6 +- modules/nf-core/bcftools/stats/main.nf | 4 +- .../bcftools/stats/tests/main.nf.test.snap | 68 ++++----- modules/nf-core/bcftools/stats/tests/tags.yml | 2 - modules/nf-core/fastp/environment.yml | 3 +- modules/nf-core/fastp/main.nf | 4 +- modules/nf-core/fastp/tests/main.nf.test.snap | 144 +++++++++--------- modules/nf-core/fastp/tests/tags.yml | 2 - .../nf-core/samtools/faidx/environment.yml | 6 +- modules/nf-core/samtools/faidx/main.nf | 4 +- .../samtools/faidx/tests/main.nf.test.snap | 72 ++++----- modules/nf-core/samtools/faidx/tests/tags.yml | 2 - .../nf-core/samtools/flagstat/environment.yml | 6 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test.snap | 20 +-- .../nf-core/samtools/flagstat/tests/tags.yml | 2 - .../nf-core/samtools/idxstats/environment.yml | 6 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test.snap | 20 +-- .../nf-core/samtools/idxstats/tests/tags.yml | 2 - .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/main.nf.test.snap | 58 +++---- modules/nf-core/samtools/index/tests/tags.yml | 2 - modules/nf-core/samtools/sort/environment.yml | 6 +- modules/nf-core/samtools/sort/main.nf | 7 +- .../samtools/sort/tests/main.nf.test.snap | 66 ++++---- .../nf-core/samtools/stats/environment.yml | 6 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../samtools/stats/tests/main.nf.test.snap | 48 +++--- modules/nf-core/samtools/stats/tests/tags.yml | 2 - nextflow.config | 2 +- ro-crate-metadata.json | 49 ++++-- .../tests/main.nf.test.snap | 96 ++++++------ .../nf-core/bam_stats_samtools/tests/tags.yml | 2 - tests/default.nf.test.snap | 124 +++++++-------- 56 files changed, 582 insertions(+), 549 deletions(-) delete mode 100644 modules/nf-core/bcftools/filter/tests/tags.yml delete mode 100644 modules/nf-core/bcftools/index/tests/tags.yml delete mode 100644 modules/nf-core/bcftools/query/tests/tags.yml delete mode 100644 modules/nf-core/bcftools/sort/tests/tags.yml delete mode 100644 modules/nf-core/bcftools/stats/tests/tags.yml delete mode 100644 modules/nf-core/fastp/tests/tags.yml delete mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml delete mode 100644 modules/nf-core/samtools/flagstat/tests/tags.yml delete mode 100644 modules/nf-core/samtools/idxstats/tests/tags.yml delete mode 100644 modules/nf-core/samtools/index/tests/tags.yml delete mode 100644 modules/nf-core/samtools/stats/tests/tags.yml delete mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/tags.yml diff --git a/.nf-core.yml b/.nf-core.yml index fd14fab8..2797c1f7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ template: name: bactmap description: A mapping-based pipeline for bacterial whole genome sequences author: Andries J. van Tonder - version: 2.0.0dev + version: 2.0.0 force: true outdir: . skip_features: [] diff --git a/CHANGELOG.md b/CHANGELOG.md index 737d16df..d7675169 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.0.0dev - [date] +## 2.0.0 - Titanium Bird - 2025-09-15 nf-core/bactmap release v2.0.0. The pipeline has been completely rewritten using a fresh template created with [nf-core](https://nf-co.re/). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f048e363..622e1845 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,9 +1,10 @@ # multiqc_config.yml report_comment: > - This report has been generated by the nf-core/bactmap - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/bactmap analysis pipeline. For information about how + to interpret these results, please see the documentation. # Report section order report_section_order: @@ -106,7 +107,8 @@ top_modules: anchor: "filtlong" target: "Filtlong" doi: "10.1371/journal.pcbi.1010905" - info: "This section of the report shows Filtlong results for reads after length filtering." + info: "This section of the report shows Filtlong results for reads after length + filtering." path_filters: - "*filtlong/*" extra: | @@ -129,7 +131,8 @@ top_modules: anchor: "samtools" target: "SAMTools" doi: "10.1093/bioinformatics/btp352" - info: "This section of the report shows SAMTools counts/statistics after mapping with Bowtie 2/BWA 2 mem." + info: "This section of the report shows SAMTools counts/statistics after mapping + with Bowtie 2/BWA 2 mem." path_filters: - "*.stats" - "bcftools": @@ -137,7 +140,8 @@ top_modules: anchor: "bcftools" target: "BCFTools" doi: "10.1093/bioinformatics/btp352" - info: "This section of the report shows BCFTools stats results for the called variants." + info: "This section of the report shows BCFTools stats results for the called + variants." path_filters: - "*.txt" diff --git a/modules.json b/modules.json index d882ed32..05bcf1bc 100644 --- a/modules.json +++ b/modules.json @@ -12,27 +12,27 @@ }, "bcftools/filter": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", "installed_by": ["modules"] }, "bcftools/index": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", "installed_by": ["bam_variant_calling_sort_freebayes_bcftools"] }, "bcftools/query": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", "installed_by": ["bam_variant_calling_sort_freebayes_bcftools"] }, "bcftools/stats": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", "installed_by": ["modules"] }, "bedtools/subtract": { @@ -72,7 +72,7 @@ }, "fastp": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["modules"] }, "fastqc": { @@ -132,32 +132,32 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "e89ff68a46b848c4d8aabb8569767516d46db319", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["bam_stats_samtools", "modules"] }, "seqtk/comp": { @@ -176,7 +176,7 @@ "nf-core": { "bam_stats_samtools": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index 55748860..ba863b38 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index e7a24ae4..920eed37 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_FILTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap index a9f51f98..7f4d423b 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap @@ -17,7 +17,7 @@ ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ @@ -34,15 +34,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:24.959966433" + "timestamp": "2025-09-11T14:11:35.716305" }, "sarscov2 - vcf_gz_index_tbi - stub": { "content": [ @@ -67,7 +67,7 @@ ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ @@ -89,15 +89,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:50.239958906" + "timestamp": "2025-09-11T14:11:54.386135" }, "vcf": { "content": [ @@ -117,7 +117,7 @@ ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ @@ -134,15 +134,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:21:54.690638665" + "timestamp": "2025-09-11T14:11:13.726932" }, "bcf output": { "content": [ @@ -162,7 +162,7 @@ ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ @@ -179,15 +179,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:20.154869487" + "timestamp": "2025-09-11T14:11:31.219355" }, "sarscov2 - vcf_gz_index": { "content": [ @@ -211,14 +211,14 @@ ], [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:01.831439795" + "timestamp": "2025-09-11T14:11:18.126698" }, "sarscov2 - vcf_gz_index_csi": { "content": [ @@ -242,14 +242,14 @@ ], [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:05.859541512" + "timestamp": "2025-09-11T14:11:22.522678" }, "vcf - stub": { "content": [ @@ -269,7 +269,7 @@ ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ @@ -286,15 +286,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:32.075222142" + "timestamp": "2025-09-11T14:11:40.997176" }, "sarscov2 - vcf_gz_index - stub": { "content": [ @@ -319,7 +319,7 @@ ] ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ [ @@ -341,15 +341,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:36.252356698" + "timestamp": "2025-09-11T14:11:45.224157" }, "sarscov2 - vcf_gz_index_csi - stub": { "content": [ @@ -374,7 +374,7 @@ ] ], "3": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ], "csi": [ [ @@ -396,15 +396,15 @@ ] ], "versions": [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:43.303679805" + "timestamp": "2025-09-11T14:11:49.650863" }, "sarscov2 - vcf_gz_index_tbi": { "content": [ @@ -428,13 +428,13 @@ ] ], [ - "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a" + "versions.yml:md5,66d244ab9257f8ac147f43946e2e751d" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:22:13.144377611" + "timestamp": "2025-09-11T14:11:26.846112" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/tags.yml b/modules/nf-core/bcftools/filter/tests/tags.yml deleted file mode 100644 index d5e01080..00000000 --- a/modules/nf-core/bcftools/filter/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/filter: - - "modules/nf-core/bcftools/filter/**" diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml index 55748860..ba863b38 100644 --- a/modules/nf-core/bcftools/index/environment.yml +++ b/modules/nf-core/bcftools/index/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 66d824a1..16ff775a 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/tests/main.nf.test.snap b/modules/nf-core/bcftools/index/tests/main.nf.test.snap index 19cdce7a..30f6f7c3 100644 --- a/modules/nf-core/bcftools/index/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/index/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ], "csi": [ [ @@ -28,15 +28,15 @@ ], "versions": [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:27:09.068494316" + "timestamp": "2025-09-11T14:12:33.825153" }, "sarscov2 - vcf - tbi": { "content": [ @@ -49,14 +49,14 @@ ] ], [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:27:02.067535809" + "timestamp": "2025-09-11T14:12:28.804939" }, "sarscov2 - vcf - tbi - stub": { "content": [ @@ -73,7 +73,7 @@ ] ], "2": [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ], "csi": [ @@ -87,15 +87,15 @@ ] ], "versions": [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:27:13.198252226" + "timestamp": "2025-09-11T14:12:38.852782" }, "sarscov2 - vcf - csi": { "content": [ @@ -108,13 +108,13 @@ ] ], [ - "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e" + "versions.yml:md5,cea31a4d868054c7308a4129232a1f0e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T13:26:58.059916648" + "timestamp": "2025-09-11T14:12:24.498904" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/index/tests/tags.yml b/modules/nf-core/bcftools/index/tests/tags.yml deleted file mode 100644 index b4c349be..00000000 --- a/modules/nf-core/bcftools/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/index: - - "modules/nf-core/bcftools/index/**" diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index 55748860..ba863b38 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 52be34b1..91e0880b 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap index beee2ef2..0e638158 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap @@ -10,27 +10,27 @@ ] ], [ - "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6" + "versions.yml:md5,0a0bd969f3e1b1dfc5617547cf2d9b6e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:09:16.570707353" + "timestamp": "2025-09-11T14:40:03.990658" }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ "out.txt", [ - "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6" + "versions.yml:md5,0a0bd969f3e1b1dfc5617547cf2d9b6e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:09:23.462432361" + "timestamp": "2025-09-11T14:40:08.930802" }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -43,13 +43,13 @@ ] ], [ - "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6" + "versions.yml:md5,0a0bd969f3e1b1dfc5617547cf2d9b6e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:09:09.337957177" + "timestamp": "2025-09-11T14:39:59.366475" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/query/tests/tags.yml b/modules/nf-core/bcftools/query/tests/tags.yml deleted file mode 100644 index fb9455cb..00000000 --- a/modules/nf-core/bcftools/query/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/query: - - "modules/nf-core/bcftools/query/**" diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 55748860..ba863b38 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 6cbd09b5..294d476c 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap index f092dbf5..3cbca56c 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -22,7 +22,7 @@ ], "3": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ], "csi": [ @@ -44,15 +44,15 @@ ] ], "versions": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:26.694501734" + "timestamp": "2025-09-11T14:49:07.959267" }, "vcf": { "content": [ @@ -72,7 +72,7 @@ ], "3": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ], "csi": [ @@ -89,15 +89,15 @@ ] ], "versions": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:10:49.218451505" + "timestamp": "2025-09-11T14:48:35.236174" }, "sarscov2 - vcf_gz_index": { "content": [ @@ -121,14 +121,14 @@ ], [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:10:56.259159613" + "timestamp": "2025-09-11T14:48:39.95133" }, "sarscov2 - vcf_gz_index_csi": { "content": [ @@ -152,14 +152,14 @@ ], [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:00.358141543" + "timestamp": "2025-09-11T14:48:44.50977" }, "sarscov2 - vcf_gz_index - stub": { "content": [ @@ -184,7 +184,7 @@ ] ], "3": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ], "csi": [ [ @@ -206,15 +206,15 @@ ] ], "versions": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:18.590986384" + "timestamp": "2025-09-11T14:48:58.749279" }, "sarscov2 - vcf_gz_index_csi - stub": { "content": [ @@ -239,7 +239,7 @@ ] ], "3": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ], "csi": [ [ @@ -261,15 +261,15 @@ ] ], "versions": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:22.65765844" + "timestamp": "2025-09-11T14:49:03.283017" }, "sarscov2 - vcf - stub": { "content": [ @@ -289,7 +289,7 @@ ], "3": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ], "csi": [ @@ -306,15 +306,15 @@ ] ], "versions": [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:11.501401617" + "timestamp": "2025-09-11T14:48:54.113947" }, "sarscov2 - vcf_gz_index_tbi": { "content": [ @@ -338,13 +338,13 @@ ] ], [ - "versions.yml:md5,54b077078de3c204fb81688af4aae489" + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:07.401740499" + "timestamp": "2025-09-11T14:48:48.979311" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/tags.yml b/modules/nf-core/bcftools/sort/tests/tags.yml deleted file mode 100644 index 6e9520dd..00000000 --- a/modules/nf-core/bcftools/sort/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/sort: - - "modules/nf-core/bcftools/sort/**" diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 7aa06d0f..ba863b38 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 - - bioconda::htslib=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index fb556e0a..8eba6cde 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap index c771a055..cc33ddc2 100644 --- a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - vcf_gz - reference": { "content": [ [ - "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --fasta-ref genome.fasta test.vcf.gz", "#", "# Definition of sets:", @@ -12,14 +12,14 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:12:00.636338532" + "timestamp": "2025-09-11T14:58:10.684378" }, "sarscov2 - vcf_gz - exons": { "content": [ [ - "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --exons exons.tsv.gz test.vcf.gz", "#", "# Definition of sets:", @@ -29,26 +29,26 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:56.472662944" + "timestamp": "2025-09-11T14:58:05.803224" }, "versions": { "content": [ [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:38.17663878" + "timestamp": "2025-09-11T14:57:51.913799" }, "sarscov2 - vcf_gz - targets": { "content": [ [ - "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --targets-file test2.targets.tsv.gz test.vcf.gz", "#", "# Definition of sets:", @@ -58,33 +58,33 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:49.263021261" + "timestamp": "2025-09-11T14:58:01.121472" }, "regions_versions": { "content": [ [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:45.263363932" + "timestamp": "2025-09-11T14:57:56.503606" }, "targets_versions": { "content": [ [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:49.260150422" + "timestamp": "2025-09-11T14:58:01.116272" }, "sarscov2 - vcf_gz - stub": { "content": [ @@ -98,7 +98,7 @@ ] ], "1": [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ], "stats": [ [ @@ -109,44 +109,44 @@ ] ], "versions": [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:12:07.469893476" + "timestamp": "2025-09-11T14:58:15.742817" }, "exon_versions": { "content": [ [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:56.46980859" + "timestamp": "2025-09-11T14:58:05.795248" }, "ref_versions": { "content": [ [ - "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4" + "versions.yml:md5,d901f4d7a114504db1dc5bc36f27f386" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:12:00.633746007" + "timestamp": "2025-09-11T14:58:10.679821" }, "sarscov2 - vcf_gz": { "content": [ [ - "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats test.vcf.gz", "#", "# Definition of sets:", @@ -156,14 +156,14 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:38.184907984" + "timestamp": "2025-09-11T14:57:51.945138" }, "sarscov2 - vcf_gz - regions": { "content": [ [ - "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.", + "# This file was produced by bcftools stats (1.22+htslib-1.22.1) and can be plotted using plot-vcfstats.", "# The command line was:\tbcftools stats --regions-file test3.vcf.gz test.vcf.gz", "#", "# Definition of sets:", @@ -173,8 +173,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-04-01T14:11:45.266296334" + "timestamp": "2025-09-11T14:57:56.50867" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/tests/tags.yml b/modules/nf-core/bcftools/stats/tests/tags.yml deleted file mode 100644 index 53c12d92..00000000 --- a/modules/nf-core/bcftools/stats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/stats: - - "modules/nf-core/bcftools/stats/**" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 90adcd2c..0c36eed2 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastp=0.24.0 + # renovate: datasource=conda depName=bioconda/fastp + - bioconda::fastp=1.0.1 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 6e3e6c43..ecac5b92 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -4,8 +4,8 @@ process FASTP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/889a182b8066804f4799f3808a5813ad601381a8a0e3baa4ab8d73e739b97001/data' : - 'community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/527b18847a97451091dba07a886b24f17f742a861f9f6c9a6bfb79d4f1f3bf9d/data' : + 'community.wave.seqera.io/library/fastp:1.0.1--c8b87fe62dcc103c' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index 9e2aaf31..5b5eeb6c 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ], "6": [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ], "html": [ [ @@ -78,15 +78,15 @@ ], "versions": [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ] } ], "meta": { "nf-test": "0.9.2", - 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"nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-03-31T13:40:28.086573661" + "timestamp": "2025-09-11T09:55:23.871395" }, "test_fastp_paired_end_trim_fail - stub": { "content": [ @@ -1060,7 +1060,7 @@ ], "6": [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ], "html": [ [ @@ -1118,15 +1118,15 @@ ], "versions": [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-03-31T13:40:35.606162029" + "timestamp": "2025-09-11T09:55:28.399328" }, "fastp test_fastp_interleaved": { "content": [ @@ -1145,18 +1145,18 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,101003b8ac634ca5fd381656ac2b8b9f" + "test.fastp.json:md5,c4e4093a100ef3fa9740620d42bf90c4" ] ], [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-03-31T13:39:23.114582408" + "timestamp": "2025-09-11T09:54:35.970659" }, "test_fastp_single_end_trim_fail": { "content": [ @@ -1166,7 +1166,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,d721f75d68a382c819b6499e6325a942" + "test.fastp.json:md5,27307e0f9154fc37e1cb84f207bf33e0" ] ], [ @@ -1191,14 +1191,14 @@ ], [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-03-31T13:39:30.757538842" + "timestamp": "2025-09-11T09:54:40.611616" }, "test_fastp_paired_end_qc_only": { "content": [ @@ -1208,7 +1208,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,1ad31d6559ff5d4d275f501f3f5c02b9" + "test.fastp.json:md5,f411d75c34448fcad813ccd9b3d0fa3d" ] ], [ @@ -1230,14 +1230,14 @@ ], [ - "versions.yml:md5,3799377c4173131ba9392346e1c40bb9" + "versions.yml:md5,c4974822658d02533e660fae343f281b" ] ], "meta": { "nf-test": "0.9.2", - 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conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 6de0095d..ed2d70a6 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 73722414..3be7b824 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ @@ -42,15 +42,15 @@ ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:31:48.258623157" + "timestamp": "2025-09-10T13:09:38.874686" }, "test_samtools_faidx_get_sizes_bgzip - stub": { "content": [ @@ -83,7 +83,7 @@ ] ], "4": [ - "versions.yml:md5,e3e4ba35a02020d173be8d1ee04eaebf" + "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08" ], "fa": [ @@ -113,15 +113,15 @@ ] ], "versions": [ - "versions.yml:md5,e3e4ba35a02020d173be8d1ee04eaebf" + "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:41.122428188" + "timestamp": "2025-09-10T13:10:10.958397" }, "test_samtools_faidx_get_sizes": { "content": [ @@ -149,7 +149,7 @@ ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ @@ -174,15 +174,15 @@ ] ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:34:02.353546697" + "timestamp": "2025-09-10T13:09:59.237249" }, "test_samtools_faidx_bgzip": { "content": [ @@ -212,7 +212,7 @@ ] ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ @@ -239,15 +239,15 @@ ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:31:55.157487176" + "timestamp": "2025-09-10T13:09:42.949204" }, "test_samtools_faidx_fasta": { "content": [ @@ -271,7 +271,7 @@ ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ [ @@ -292,15 +292,15 @@ ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:02.149455586" + "timestamp": "2025-09-10T13:09:46.914038" }, "test_samtools_faidx_get_sizes - stub": { "content": [ @@ -328,7 +328,7 @@ ], "4": [ - "versions.yml:md5,e3e4ba35a02020d173be8d1ee04eaebf" + "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08" ], "fa": [ @@ -353,15 +353,15 @@ ] ], "versions": [ - "versions.yml:md5,e3e4ba35a02020d173be8d1ee04eaebf" + "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:34.29376776" + "timestamp": "2025-09-10T13:10:06.961912" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -385,7 +385,7 @@ ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ [ @@ -406,15 +406,15 @@ ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:09.125065185" + "timestamp": "2025-09-10T13:09:51.226016" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -438,7 +438,7 @@ ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ @@ -459,15 +459,15 @@ ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:16.274287863" + "timestamp": "2025-09-10T13:09:55.423005" }, "test_samtools_faidx_get_sizes_bgzip": { "content": [ @@ -500,7 +500,7 @@ ] ], "4": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ], "fa": [ @@ -530,14 +530,14 @@ ] ], "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2024-11-20T17:32:28.117654855" + "timestamp": "2025-09-10T13:10:03.04872" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml deleted file mode 100644 index e4a83948..00000000 --- a/modules/nf-core/samtools/faidx/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/faidx: - - modules/nf-core/samtools/faidx/** diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 62054fc9..89e12a64 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index c23f3a5c..9e718431 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 04c3852b..79960bcb 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc" ], "flagstat": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:02:58.866491759" + "timestamp": "2025-09-10T13:31:17.098789" }, "BAM": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc" ], "flagstat": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:02:47.383332837" + "timestamp": "2025-09-10T13:31:12.661288" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml deleted file mode 100644 index 2d2b7255..00000000 --- a/modules/nf-core/samtools/flagstat/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/flagstat: - - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 62054fc9..89e12a64 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 3d5bf4bd..9181a1a5 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 2cc89a3b..d3e785e0 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + "versions.yml:md5,6da44e5235401559cea62052bdc0197b" ], "idxstats": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + "versions.yml:md5,6da44e5235401559cea62052bdc0197b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:11:56.466856235" + "timestamp": "2025-09-10T13:47:35.796569" }, "bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + "versions.yml:md5,6da44e5235401559cea62052bdc0197b" ], "idxstats": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + "versions.yml:md5,6da44e5235401559cea62052bdc0197b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:11:46.311550359" + "timestamp": "2025-09-10T13:47:31.86415" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml deleted file mode 100644 index d3057c61..00000000 --- a/modules/nf-core/samtools/idxstats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/idxstats: - - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 62054fc9..89e12a64 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 7019a72e..a77ad821 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 72d65e81..3836c6bf 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:21:25.261127166" + "timestamp": "2025-09-10T14:13:38.25787" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:21:12.653194876" + "timestamp": "2025-09-10T14:13:34.496412" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:21:01.854932651" + "timestamp": "2025-09-10T14:13:25.934431" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:20:51.485364222" + "timestamp": "2025-09-10T14:13:22.262088" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:20:40.518873972" + "timestamp": "2025-09-10T14:13:18.191664" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:20:21.184050361" + "timestamp": "2025-09-10T14:13:08.51539" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml deleted file mode 100644 index e0f58a7a..00000000 --- a/modules/nf-core/samtools/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/index: - - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 62054fc9..89e12a64 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 6c436c04..d4bd5a32 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta) , path(bam) @@ -30,7 +30,7 @@ process SAMTOOLS_SORT { extension = args.contains("--output-fmt sam") ? "sam" : args.contains("--output-fmt cram") ? "cram" : "bam" - reference = fasta ? "--reference ${fasta}" : "" + def reference = fasta ? "--reference ${fasta}" : "" output_file = index_format ? "${prefix}.${extension}##idx##${prefix}.${extension}.${index_format} --write-index" : "${prefix}.${extension}" if (index_format) { if (!index_format.matches('bai|csi|crai')) { @@ -65,7 +65,6 @@ process SAMTOOLS_SORT { extension = args.contains("--output-fmt sam") ? "sam" : args.contains("--output-fmt cram") ? "cram" : "bam" - def reference = fasta ? "--reference ${fasta}" : "" if (index_format) { if (!index_format.matches('bai|csi|crai')) { error "Index format not one of bai, csi, crai." diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 84e72802..473e1745 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:40.803476526" + "timestamp": "2025-09-10T14:43:31.395604" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ], "6": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ], "bai": [ @@ -84,7 +84,7 @@ ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], @@ -92,7 +92,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:46.797296642" + "timestamp": "2025-09-10T14:43:37.387063" }, "bam_csi_index": { "content": [ @@ -102,7 +102,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,d9645c9b6d7f991426d47ad80c275ef7" + "test.sorted.bam:md5,72ca1dff5344a5e5e6b892fe5f6b134d" ] ], [ @@ -111,18 +111,18 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,124e6600a0a811227c43fd6864c72902" + "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8" ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:13.394881233" + "timestamp": "2025-09-10T14:43:06.976036" }, "multiple bam bai index": { "content": [ @@ -132,7 +132,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,0669e48038989db924a9f2957e26317c" + "test.sorted.bam:md5,3ffa2affc29f0aa6e7b36dded84625fe" ] ], [ @@ -145,14 +145,14 @@ ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:28.192036852" + "timestamp": "2025-09-10T14:43:18.72271" }, "cram - stub": { "content": [ @@ -182,7 +182,7 @@ ], "6": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ], "bai": [ @@ -209,7 +209,7 @@ ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], @@ -217,7 +217,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:58.847704746" + "timestamp": "2025-09-10T14:43:48.734367" }, "multiple bam": { "content": [ @@ -227,21 +227,21 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,c6ab045cc495485d3819bd44c5d69b92" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], [ ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T14:00:50.550947084" + "timestamp": "2025-09-10T14:43:12.989244" }, "multiple bam - stub": { "content": [ @@ -252,7 +252,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,c6ab045cc495485d3819bd44c5d69b92" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], "1": [ @@ -271,7 +271,7 @@ ], "6": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ], "bai": [ @@ -282,7 +282,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,c6ab045cc495485d3819bd44c5d69b92" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], "crai": [ @@ -298,7 +298,7 @@ ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], @@ -306,7 +306,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T14:02:05.837266709" + "timestamp": "2025-09-10T14:43:43.196638" }, "bam_no_index": { "content": [ @@ -316,21 +316,21 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,7fa751088f8d86c2685fb50a8b90f53f" + "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e" ] ], [ ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T14:00:20.988801663" + "timestamp": "2025-09-10T14:42:54.926504" }, "multiple bam csi index": { "content": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,3fe979e8bd453d33224706d1478df7a1" + "test.sorted.bam:md5,295503ba5342531a3310c33ad0efbc22" ] ], [ @@ -353,14 +353,14 @@ ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:34.591655792" + "timestamp": "2025-09-10T14:43:25.059178" }, "bam": { "content": [ @@ -400,7 +400,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,31e1c0224336156ea9ca81dcfe23356d" + "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54" ] ], [ @@ -409,17 +409,17 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,0575b098cbea8c3af1f58d2a83efa07f" + "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0" ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-13T16:39:06.968372189" + "timestamp": "2025-09-10T14:43:00.82974" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 62054fc9..89e12a64 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4443948b..c06ad3bf 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index df507be7..a451c04e 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba" ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba" ] ], "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T09:29:16.767396182" + "timestamp": "2025-09-10T15:05:52.878044" }, "bam - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ], "stats": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T09:29:29.721580274" + "timestamp": "2025-09-10T15:05:56.722672" }, "cram - stub": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ], "stats": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T09:29:53.567964304" + "timestamp": "2025-09-10T15:06:13.766719" }, "bam": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,d53a2584376d78942839e9933a34d11b" + "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9" ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ], "stats": [ [ @@ -125,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,d53a2584376d78942839e9933a34d11b" + "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9" ] ], "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T09:28:50.73610604" + "timestamp": "2025-09-10T15:05:30.301153" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml deleted file mode 100644 index 7c28e30f..00000000 --- a/modules/nf-core/samtools/stats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/stats: - - modules/nf-core/samtools/stats/** diff --git a/nextflow.config b/nextflow.config index b2797c73..4dc9aa87 100644 --- a/nextflow.config +++ b/nextflow.config @@ -324,7 +324,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.10.5' - version = '2.0.0dev' + version = '2.0.0' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8fad34f7..85cb3b04 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2025-03-13T14:15:46+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2025-09-15T13:47:58+00:00", "description": "

\n \n \n \"nf-core/bactmap\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/bactmap/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/bactmap/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/bactmap/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/bactmap/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bactmap/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/bactmap)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bactmap-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bactmap)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/bactmap** is a bioinformatics best-practice analysis pipeline for mapping short (Illumina) and long reads (Oxford Nanopore) from bacterial WGS to a reference sequence, creating filtered VCF files and making pseudogenomes based on high quality positions in the VCF files.\n\n## Pipeline summary\n\n![](docs/images/bactmap_pipeline.png)\n\n1. Index reference fasta file (short-read: [`BWA index`](https://github.com/lh3/bwa) or [`Bowtie2 build`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml); long-read: [`minimap2 index`](https://github.com/lh3/minimap2))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`falco`](https://github.com/smithlabcode/falco) as an alternative option)\n3. Calculate fastq summary statistics ([`fastq-scan`](https://github.com/rpetit3/fastq-scan))\n4. Perform read pre-processing (optional)\n - Adapter clipping and merging (short-read: [`fastp`](https://github.com/OpenGene/fastp) or [`AdapterRemoval2`](https://github.com/MikkelSchubert/adapterremoval); long-read: [`porechop`](https://github.com/rrwick/Porechop) or [`Porechop_ABI`](https://github.com/bonsai-team/Porechop_ABI))\n - Quality filtering (long-read: [`Filtlong`](https://github.com/rrwick/Filtlong)), [`Nanoq`](https://github.com/esteinig/nanoq)\n - Run merging ([`cat`](https://pubs.opengroup.org/onlinepubs/9699919799/utilities/cat.html))\n5. Downsample fastq files (optional) ([`Rasusa`](https://github.com/mbhall88/rasusa))\n6. Summarise read statistics pre- and post-processing and subsampling ([`read_stats`](https://github.com/nf-core/bactmap/blob/master/modules/local/read_stats/main.nf))\n7. Variant calling\n\n- Map reads to reference (short-read: [`BWA-MEM2`](https://github.com/bwa-mem2/bwa-mem2) or [`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml); long-read: [`minimap2`](https://github.com/lh3/minimap2))\n- Sort and index alignments ([`SAMtools view/sort`](https://sourceforge.net/projects/samtools/files/samtools/))\n- Summarise alignment statistics ([`SAMtools stats`](https://sourceforge.net/projects/samtools/files/samtools/))\n- Call variants (short-read: [`FreeBayes`](https://github.com/freebayes/freebayes); long-read: [`Clair3`](https://github.com/HKU-BAL/Clair3))\n- Filter variants ([`BCFtools filter`](http://samtools.github.io/bcftools/bcftools.html))\n- Summarise variant statistics ([`BCFtools stats`](http://samtools.github.io/bcftools/bcftools.html))\n- Convert filtered bcf to pseudogenome fasta ([`BCFtools consensus`](http://samtools.github.io/bcftools/bcftools.html) and [`BEDtools`](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html))\n- Summarise mapping statistics ([`seqtk`](https://github.com/lh3/seqtk))\n\n8. Create alignment from pseudogenomes by concatenating fasta files having first checked that the sample sequences are high quality ([`alignpseudogenomes`](https://github.com/nf-core/bactmap/blob/master/modules/local/alignpseudogenomes/main.nf))\n9. Extract variant sites from alignment ([`SNP-sites`](https://github.com/sanger-pathogens/snp-sites))\n10. Present QC for raw and processed reads, alignment statistics and variant statistics ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n```csv title=\"samplesheet.csv\"\nsample,run_accession,instrument_platform,fastq_1,fastq_2\n2612,run1,ILLUMINA,2612_run1_R1.fq.gz,\n2613,run1,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz\n2614,run3,OXFORD_NANOPORE,2614_file1.fastq.gz,\n2614,run3,OXFORD_NANOPORE,2614_file2.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end), either Illumina (short reads) or Oxford Nanopore (long reads).\n\nAdditionally, if you are analysing Oxford Nanopore data, you will need to provide the path to a model to use with `Clair3` (specified with `--clair3_model`). Models for older chemistries and basecallers (e.g. r9.4.1) can be downloaded from [here](https://www.bio8.cs.hku.hk/clair3/clair3_models/). For newer chemistries and basecallers, ONT provides models through [Rerio](https://github.com/nanoporetech/rerio). To download the models for Clair3 from the ONT github, you can use the following commands (each model will be downloaded to the folder `clair3_models/`):\n\n```bash\n# Clone the rerio repository\ngit clone https://github.com/nanoporetech/rerio\n\n# Download all models\npython3 download_model.py --clair3\n```\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/bactmap \\\n -profile \\\n --input samplesheet.csv \\\n --fasta \\\n --clair3_model \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/bactmap/usage) and the [parameter documentation](https://nf-co.re/bactmap/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/bactmap/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/bactmap/output).\n\n## Credits\n\nnf-core/bactmap was originally written by [Anthony Underwood](https://github.com/antunderwood), [Andries van Tonder](https://github.com/avantonder) and [Thanh Le Viet](https://github.com/thanhleviet).\n\nWe thank the following people for their extensive assistance in the development\nof this pipeline:\n\n- [Alexandre Gilardet](https://github.com/alexandregilardet)\n- [Hanh Hoang](https://github.com/sainsachiko)\n- [Ismael Henarejos-Castilo](https://github.com/IsmaelHC1994)\n- [Mareike Janiak](https://github.com/MareikeJaniak)\n- [Harshil Patel](https://github.com/drpatelh)\n- [Olha Petryk](https://github.com/opetryk)\n- [Richard Agyekum](https://github.com/QuadjoLegend)\n- [Steven Sutcliffe](https://github.com/sgsutcliffe)\n- [Szymon Szyszkowski](https://github.com/project-defiant)\n\nAnthony Underwood's time working on the project was funded by the National Institute for Health Research(NIHR) Global Health Research Unit for the Surveillance of Antimicrobial Resistance (Grant Reference Number 16/136/111)\n![NIHR funded](assets/nihr_logos_funded_by.jpg)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#bactmap` channel](https://nfcore.slack.com/channels/bactmap) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -31,6 +31,9 @@ { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -43,6 +46,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +105,7 @@ }, "mentions": [ { - 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"@id": "#3f5008e2-1065-44ff-89de-ac416b610232", + "@id": "#f13981a3-764d-43b0-b4fb-474153139fca", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/bactmap", - "resource": "repos/nf-core/bactmap/actions/workflows/ci.yml", + "resource": "repos/nf-core/bactmap/actions/workflows/nf-test.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, @@ -208,6 +219,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -228,6 +244,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -313,6 +334,12 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#ajv37@shgb2monitor.vet.private.cam.ac.uk", + "@type": "Person", + "email": "ajv37@shgb2monitor.vet.private.cam.ac.uk", + "name": "Andries Van Tonder" } ] } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index 8ca22526..fa4a194c 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -30,9 +30,9 @@ ] ], "3": [ - 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"test.stats:md5,291bb2393ec947140d12d42c2795b222" + "test.stats:md5,7a05a22bdb17e8df6e8c2d100ff09a31" ] ], [ - "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", - "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", - "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" + "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", + "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:07:49.731645858" + "timestamp": "2025-09-10T13:37:27.672053" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +291,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" + "test.stats:md5,a391612b5ef5b181e854ccaad8c8a068" ] ], [ - "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", - "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", - "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" + "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", + "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" ] ], "meta": { - 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- subworkflows/nf-core/bam_stats_samtools/** diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 99386271..562b7a35 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -10,16 +10,16 @@ "bcftools": 1.2 }, "BCFTOOLS_FILTER": { - "bcftools": 1.21 + "bcftools": 1.22 }, "BCFTOOLS_INDEX": { - "bcftools": 1.21 + "bcftools": 1.22 }, "BCFTOOLS_SORT": { - "bcftools": 1.21 + "bcftools": 1.22 }, "BCFTOOLS_STATS": { - "bcftools": 1.21 + "bcftools": 1.22 }, "BEDTOOLS_GENOMECOV": { "bedtools": "2.31.1" @@ -36,7 +36,7 @@ "bowtie2": "2.5.4" }, "FASTP_PAIRED": { - "fastp": "0.24.0" + "fastp": "1.0.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -81,22 +81,22 @@ "sed": 4.9 }, "SAMTOOLS_FAIDX": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_INDEX": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_SORT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_STATS": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SEQTK_COMP": { "seqtk": "1.4-r122" @@ -105,7 +105,7 @@ "seqtk_parser.py": 1.0 }, "Workflow": { - "nf-core/bactmap": "v2.0.0dev" + "nf-core/bactmap": "v2.0.0" } }, [ @@ -396,18 +396,18 @@ [ "01.fa:md5,17e6433115d1ad1b4ffdf384d783dc29", "02.fa:md5,9048642262df13a6fc427b2d971b7546", - "01.filtered.vcf.gz:md5,2ef834266f3700f4fe177e6a9577c694", + "01.filtered.vcf.gz:md5,9f24409ae4638b0ed0fa8891bec1659b", "01.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905", - "02.filtered.vcf.gz:md5,23e76ab630672beb97de05d38d9da5e8", + "02.filtered.vcf.gz:md5,1253ca69cd259bdf2f14a378a4df96e5", "02.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905", "01.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "02.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "01.sorted.vcf.gz:md5,737e9fa6c59c5c1333db08d4c9d8670b", + "01.sorted.vcf.gz:md5,b70e6dd2223d07d8d233d9eb54f16fb1", "01.sorted.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905", - "02.sorted.vcf.gz:md5,d24abc555c724569fd55ea11db938efc", + "02.sorted.vcf.gz:md5,208451945ce7c9be754fea959aa083c1", "02.sorted.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905", - "01.bcftools_stats.txt:md5,8f9bcfedbacf4d0a81c5e06078ad68e1", - "02.bcftools_stats.txt:md5,f0ce79e8697c5149a7e313d602502361", + "01.bcftools_stats.txt:md5,defae651d5565681d95172331c428d9d", + "02.bcftools_stats.txt:md5,64ce5bc394014836c039d2f98503ee8e", "01.bed:md5,3610ca49fad02e567afc984e5ae0cce8", "02.bed:md5,37284f438898485550db0a584251e69f", "01.subtracted.bed:md5,3610ca49fad02e567afc984e5ae0cce8", @@ -421,34 +421,34 @@ "genome.fna.rev.1.bt2:md5,a1cc6383eb8d90710502a540f87bfa13", "genome.fna.rev.2.bt2:md5,871b69582268b9404cb1884a401cdc39", "versions.yml:md5,f986bc29ed66b12ac01d6a64a13c3227", - "01_test_1.fastp.html:md5,777a21c5a2501153ac793ed66ca98f6c", - "01_test_1.fastp.json:md5,3344250923cc58a7bb7f840a76051dd0", - "01_test_1.fastp.log:md5,6d6d688a242b5e5d297a4551984e2fe6", - "02_test_2.fastp.html:md5,1d04d46988edcc4b94bf509f5ae5deab", - "02_test_2.fastp.json:md5,a499231c7f816760797450f27df719e5", - "02_test_2.fastp.log:md5,93481c8b4b3eb7e673718d98e166f53a", - "01_test_1_processed_1_fastqc.html:md5,bf59a3177ded213e2caab87115ca25a5", - "01_test_1_processed_1_fastqc.zip:md5,95e0e9dfefbcb10d70a145d414fe1252", - "01_test_1_processed_2_fastqc.html:md5,aef654e482e3946e870aa625bd72187b", - "01_test_1_processed_2_fastqc.zip:md5,ebc15fb5c87ba2f67305dcea8eb937cb", - "02_test_2_processed_1_fastqc.html:md5,c9b9864501b01f69c64613b13efa7a77", - "02_test_2_processed_1_fastqc.zip:md5,24dfa5430cea573c271ad2ab6a79aab9", - "02_test_2_processed_2_fastqc.html:md5,af95db2026262a1d52eb67ec47ad9a46", - "02_test_2_processed_2_fastqc.zip:md5,971ded80b671012925c51c451cf36799", - "01_test_1_raw_1_fastqc.html:md5,b0d18399372102778dd42c9d8685515f", - "01_test_1_raw_1_fastqc.zip:md5,1cc79107eb85d45f30e30ef4879bc8b3", - "01_test_1_raw_2_fastqc.html:md5,4151281ca940d80e922ba979f811d9a8", - "01_test_1_raw_2_fastqc.zip:md5,f1134c7f00b3a6176d53a2ae0881c65d", - "02_test_2_raw_1_fastqc.html:md5,fe180d4709fa8f47bc8d4c4775f40c52", - "02_test_2_raw_1_fastqc.zip:md5,25d10fc3441dd7d96f638452ef5268bd", - "02_test_2_raw_2_fastqc.html:md5,b5bd8d94c85b0d8a216e12be063effa2", - "02_test_2_raw_2_fastqc.zip:md5,1cc8af2eb1333db4f1de820346af7af2", + "01_test_1.fastp.html:md5,14e71d9c1f15f781897369739c461176", + "01_test_1.fastp.json:md5,8c5669f673278a2178784d153de87050", + "01_test_1.fastp.log:md5,b55b929ce1d3387d19e9310fc83b4cb9", + "02_test_2.fastp.html:md5,b815b81b18cd8876e8bb1c255da785d2", + "02_test_2.fastp.json:md5,09d0c941bb86ac309d93bc24d27fbd9b", + "02_test_2.fastp.log:md5,f3c8e20f1004e380dbe89b639f462c70", + "01_test_1_processed_1_fastqc.html:md5,9bd362ca57f59414f87dff6874cc0cfc", + "01_test_1_processed_1_fastqc.zip:md5,e0e90e71511d97a735c094a83bd72134", + "01_test_1_processed_2_fastqc.html:md5,7b433a3300a18167c5ba77206f65ce29", + "01_test_1_processed_2_fastqc.zip:md5,560fe56d458e32af3a8533cece92bfe5", + "02_test_2_processed_1_fastqc.html:md5,94979e55cae0f243e7ee9ac8889baa50", + "02_test_2_processed_1_fastqc.zip:md5,774c632f16a113a663a92128615336b5", + "02_test_2_processed_2_fastqc.html:md5,6f0e819a782f2de05489cf666278186d", + "02_test_2_processed_2_fastqc.zip:md5,946cb78c801cd2fa706da3e562861d84", + "01_test_1_raw_1_fastqc.html:md5,b9a29b3ea3beaf5a3e71e5f57a2a6871", + "01_test_1_raw_1_fastqc.zip:md5,2adf6891d78ff09ebeb50300ffa1668a", + "01_test_1_raw_2_fastqc.html:md5,b2f3607d678ea3aa66685d9f6bd14617", + "01_test_1_raw_2_fastqc.zip:md5,3278ca109e0e87c66501f1b511ea6a0c", + "02_test_2_raw_1_fastqc.html:md5,be150d5833bb946e941e100756bb3e98", + "02_test_2_raw_1_fastqc.zip:md5,1b1387115d48acbf1d55749905423955", + "02_test_2_raw_2_fastqc.html:md5,56ea6990e2e0457bf1dcb1b5416c9e2b", + "02_test_2_raw_2_fastqc.zip:md5,c020a963ba6f09ef6fe02c6ae4552929", "01_test_1.processed.json:md5,125efed1942221fbf536885fbf475e66", "02_test_2.processed.json:md5,78fbdb421671f255b1c0e12cfe0653a4", "01_test_1.raw.json:md5,39066d3164d2dbdc7a198468cacaf838", "02_test_2.raw.json:md5,3cb79d84ea9de94940e4d1799c0e1c2b", - "01.vcf.gz:md5,1cddea70c563d3331959e0d3f41a24cb", - "02.vcf.gz:md5,3bb3acfad68188a3c6b9c8ad85b84374", + "01.vcf.gz:md5,1803ee1ae2773c7b85d833d435b544dc", + "02.vcf.gz:md5,293004bea2752b8f1f5f6ee8634eb374", "genome.fna:md5,dafd38f5454b54fbea38245d773062a5", "genome.mmi:md5,76c23f17ce1cade4a054bf2763b081db", "fastp-insert-size-plot.txt:md5,162036bf69d2dc7386b43f2bdadac877", @@ -467,12 +467,12 @@ "fastp_filtered_reads_plot.txt:md5,b0bb82fc4a23564c834ef8c4f4706faf", "fastqc-1-status-check-heatmap.txt:md5,2958bbda783b97cef0b64530cbdbb01d", "fastqc-1_per_base_n_content_plot.txt:md5,ab8e8d876edde1e457b3153888c88107", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,ebfcb629f7713a7de62f8cc714227258", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,64b4384f9eef2f7c6256b3df0d68d56a", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,d2a0fc017d5ba88e777c855bf89732b9", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,c2bc0602f70325f7fb82678c235ad3be", - "fastqc-1_sequence_counts_plot.txt:md5,8f0b661870c70fa37b74c81d61be0ad5", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,aa27aa03b7e4eeb2a22b8b7ac24194fe", + "fastqc-1_per_base_sequence_quality_plot.txt:md5,9e8b520d210127656adab7a734f0191e", + "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,f1542e9e7398dda884460eaf46795ff5", + "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,86db46ff07ff526eee61d9de82ed76c0", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,67c58bd6be8e3404ebc1b438d9fcbf2c", + "fastqc-1_sequence_counts_plot.txt:md5,93e8c72254cab3431a2230298d970619", + "fastqc-1_sequence_duplication_levels_plot.txt:md5,c11a44d8967bcc3fd978b70c497dbd9a", "fastqc-status-check-heatmap.txt:md5,7d06360e828f3e153a0b21051d23911b", "fastqc_per_base_n_content_plot.txt:md5,ea371a265a80840751645c2476c98754", "fastqc_per_base_sequence_quality_plot.txt:md5,6362bc88473fc3c3e6d69a650fce6b3b", @@ -481,21 +481,21 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,3e61d4e1bc67d2cf85c00d020f6a32a8", "fastqc_sequence_counts_plot.txt:md5,d1c81af14b6675c3f9f04125c1ecb484", "fastqc_sequence_duplication_levels_plot.txt:md5,e32366bc23f5fb89aa60ef7b0f29de03", - "fastqc_sequence_length_distribution_plot.txt:md5,e7bcd66dce7ca3b41a70e518608c4586", - "llms-full.txt:md5,5e27a01f696268be99afc29346fab180", - "multiqc.parquet:md5,d6cd6fce8254fded6549decf1c4a69b4", + "fastqc_sequence_length_distribution_plot.txt:md5,cb379474706e24255b725ac25b7d141e", + "llms-full.txt:md5,dd007f04c1c596fc6d2cdf44b3b41d98", + "multiqc.parquet:md5,f43674dc04859e0fd3660d488247ece1", "multiqc_bcftools_stats_bcftools.txt:md5,c3ed02e08a492df1f0f889fcd03e331d", "multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57", - "multiqc_fastp.txt:md5,d646c6b7ae38839c05130fb0b41359e6", + "multiqc_fastp.txt:md5,699888aa8b30449fc313819952c69876", "multiqc_fastqc.txt:md5,1dbca9f02b1b75f5df2ac02c81d78411", - "multiqc_fastqc_fastqc-1.txt:md5,e49ae5a350035d161d70d5fc97a0b2d6", - "multiqc_general_stats.txt:md5,123a961824ccf20f0258292694a3425d", + "multiqc_fastqc_fastqc-1.txt:md5,6fb9e3135beb3f43f193bdcb67d247b2", + "multiqc_general_stats.txt:md5,314ca8131542969bbf41ffe8be336796", "multiqc_samtools_stats_samtools.txt:md5,bc33622a9e4c162e1cb0ff5cabede2a6", "samtools-stats-dp.txt:md5,4b8fe2e0db527dc98fc21d27f2df0e11", "samtools_alignment_plot.txt:md5,164ec8a3eceb8d56809f7970f1d0290b", "01.fa:md5,ec73cef39989caf8e39d94271a64612c", "02.fa:md5,5a1b47e59b09692f7ea9d35da64c0558", - "aligned_pseudogenomes.fas:md5,bf5d42e4d26f61cbf702d30f140f74a8", + "aligned_pseudogenomes.fas:md5,335eef26460547a611e0f65e547c9432", "01.subsampled_1.fastq.gz:md5,67f961708debdc99dd25b6e45199bd5e", "01.subsampled_2.fastq.gz:md5,7d173d53ad835ed689ab7a5c5ac3d89b", "02.subsampled_1.fastq.gz:md5,c3a57b07c737ea41807a08e4d72d5100", @@ -503,16 +503,16 @@ "01_test_1.read_stats.csv:md5,ff40aaa6720a766448a3b8bde72f530f", "02_test_2.read_stats.csv:md5,c0186b0b0464a58d780334ebb63cc70a", "genome.fna.fai:md5,aa44b24652a42e538478dea3492480dd", - "01.sorted.bam:md5,4290544bd7790801d7a1c185e5198919", - "01.sorted.bam.bai:md5,4634ad8d3177a93ecec0e94335dee099", - "02.sorted.bam:md5,260382cadb5cb74be46d0797f7c07f4d", - "02.sorted.bam.bai:md5,b7143f304d3a4986963b7de92538b65c", + "01.sorted.bam:md5,dc79ff95cc093e543bb490711b961551", + "01.sorted.bam.bai:md5,194c81a937bc1defaffe2e0aa1ddd8e6", + "02.sorted.bam:md5,8ac62b020645a540c193f507086697b4", + "02.sorted.bam.bai:md5,40d3309085ab80106f2f0c67b5dab19d", "01.sorted.flagstat:md5,4f152687b9140a16a48856b0bb216289", "01.sorted.idxstats:md5,aa16d5da39ddbdc94dbeb52ed994c515", - "01.sorted.stats:md5,d0b79225c8fc7d46e56cc7ffeea612be", + "01.sorted.stats:md5,fcd22c10723786252888ec9c5f47a14a", "02.sorted.flagstat:md5,23ce0492dce1ce77e1350aa1632b1da9", "02.sorted.idxstats:md5,0670671323b7d1f14f15625c3c179b9f", - "02.sorted.stats:md5,a4b350a3569ac69e5a7a983a8c8abef4", + "02.sorted.stats:md5,76b87ccd13bd5d913deb3070063f92a7", "01.seqtk_stats.tsv:md5,589ff7dc5f0eec7f60c5a940b2500298", "02.seqtk_stats.tsv:md5,bd6fe576e5972d925ff4ec45fed17eee", "mapping_summary.tsv:md5,6107518dec4d9802ba35775df42f1e46", @@ -525,6 +525,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-11T15:10:29.302439" + "timestamp": "2025-09-15T15:01:03.587767" } } \ No newline at end of file