From 27cab9e10043cc797d2d282d471d4e021ee6f843 Mon Sep 17 00:00:00 2001 From: Ksenia Lavrichenko Date: Sun, 23 Aug 2026 19:27:12 +0200 Subject: [PATCH 1/2] update(sniffles): bump version 2.7.3 -> 2.8.0 --- .../linux_amd64-bd-c25a97c10afa095a_1.txt | 631 ++++++++++++++++++ .../linux_arm64-bd-5574c3aedf697468_1.txt | 592 ++++++++++++++++ modules/nf-core/sniffles/environment.yml | 2 +- modules/nf-core/sniffles/main.nf | 6 +- modules/nf-core/sniffles/meta.yml | 28 +- 5 files changed, 1252 insertions(+), 7 deletions(-) create mode 100644 modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-c25a97c10afa095a_1.txt create mode 100644 modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-5574c3aedf697468_1.txt diff --git a/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-c25a97c10afa095a_1.txt b/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-c25a97c10afa095a_1.txt new file mode 100644 index 000000000000..b175e4408521 --- /dev/null +++ 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BSD +size: 615477 +timestamp: 1786599613561 diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml index d9d90e951ff3..9f02ca8bd867 100644 --- a/modules/nf-core/sniffles/environment.yml +++ b/modules/nf-core/sniffles/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sniffles=2.7.3 + - bioconda::sniffles=2.8.0 diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf index 0a6fe1fc19fc..f05f12a7476c 100644 --- a/modules/nf-core/sniffles/main.nf +++ b/modules/nf-core/sniffles/main.nf @@ -3,9 +3,9 @@ process SNIFFLES { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73397171642c8f96d79b94a16d5142eee4b389473aba7a04ca4493e62aa6e4ac/data' : - 'community.wave.seqera.io/library/sniffles:2.7.3--4d6ef29e260d91be' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container +? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a392a64ae046bd1b8679f2ae590f88d84fed26d569ab70810df969741722dbcc/data' +: 'community.wave.seqera.io/library/sniffles:2.8.0--c25a97c10afa095a' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml index 85aea81739c6..f2d4211f676c 100644 --- a/modules/nf-core/sniffles/meta.yml +++ b/modules/nf-core/sniffles/meta.yml @@ -21,9 +21,7 @@ input: e.g. [ id:'test' ] - input: type: file - description: A single .bam/.cram file - OR - one or more .snf files - OR - - a single .tsv file containing a list of .snf files and optional sample - ids as input + description: A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input pattern: "*.{bam,cram,snf,tsv}" ontologies: - edam: http://edamontology.org/format_3475 @@ -125,3 +123,27 @@ maintainers: - "@christopher-hakkaart" - "@yuukiiwa" - "@fellen31" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/sniffles:2.8.0--c25a97c10afa095a + build_id: bd-c25a97c10afa095a_1 + scan_id: sc-1ed8ecc96bfef818_1 + linux/arm64: + name: community.wave.seqera.io/library/sniffles:2.8.0--5574c3aedf697468 + build_id: bd-5574c3aedf697468_1 + scan_id: sc-991b8341772825a8_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/sniffles:2.8.0--2f9e9de84854e212 + build_id: bd-2f9e9de84854e212_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/5442fefaf2312352bfc30a28db3189f6065bdaff622e235305cd7e4142323f0a/data + linux/amd64: + name: oras://community.wave.seqera.io/library/sniffles:2.8.0--78237e804565135a + build_id: bd-78237e804565135a_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a392a64ae046bd1b8679f2ae590f88d84fed26d569ab70810df969741722dbcc/data + conda: + linux/amd64: + lock_file: modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-c25a97c10afa095a_1.txt + linux/arm64: + lock_file: modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-5574c3aedf697468_1.txt From d772e6553205023381c8f8b714b668c729f27bb9 Mon Sep 17 00:00:00 2001 From: Ksenia Lavrichenko Date: Sun, 23 Aug 2026 19:30:44 +0200 Subject: [PATCH 2/2] update(sniffles): bump version 2.7.3 -> 2.8.0; update snapshots --- .../nf-core/sniffles/tests/main.nf.test.snap | 110 +++++++++--------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/modules/nf-core/sniffles/tests/main.nf.test.snap b/modules/nf-core/sniffles/tests/main.nf.test.snap index ad15335712c8..afadd0975a3c 100644 --- a/modules/nf-core/sniffles/tests/main.nf.test.snap +++ b/modules/nf-core/sniffles/tests/main.nf.test.snap @@ -30,16 +30,16 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] } ], + "timestamp": "2026-08-23T19:30:26.36794", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:49:13.462734483" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], true, false": { "content": [ @@ -48,14 +48,14 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] }, "test.vcf.gz.tbi", [ "##fileformat=VCFv4.2", - "##source=Sniffles2_2.7.3" + "##source=Sniffles2_2.8.0" ], [ "##ALT=", @@ -94,6 +94,9 @@ "##FILTER=", "##FILTER=", "##FILTER=", + "##FILTER=", + "##FILTER=", + "##FILTER=", "##INFO=", "##INFO=", "##INFO=", @@ -113,17 +116,14 @@ "##INFO=", "##INFO=", "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=" + "##INFO=" ] ], + "timestamp": "2026-08-23T19:29:24.376423", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:10.355303818" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], false, true -stub": { "content": [ @@ -146,16 +146,16 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] } ], + "timestamp": "2026-08-23T19:30:12.10492", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:56.815803593" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, bed, true, true": { "content": [ @@ -164,7 +164,7 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] }, @@ -172,7 +172,7 @@ "test.vcf.gz.tbi", [ "##fileformat=VCFv4.2", - "##source=Sniffles2_2.7.3" + "##source=Sniffles2_2.8.0" ], [ "##ALT=", @@ -211,6 +211,9 @@ "##FILTER=", "##FILTER=", "##FILTER=", + "##FILTER=", + "##FILTER=", + "##FILTER=", "##INFO=", "##INFO=", "##INFO=", @@ -230,17 +233,14 @@ "##INFO=", "##INFO=", "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=" + "##INFO=" ] ], + "timestamp": "2026-08-23T19:29:56.486401", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:39.352200695" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], true, false -stub": { "content": [ @@ -268,16 +268,16 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] } ], + "timestamp": "2026-08-23T19:30:03.342205", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:48.221342424" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], true, true -stub": { "content": [ @@ -310,16 +310,16 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] } ], + "timestamp": "2026-08-23T19:30:19.184308", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:49:06.162346127" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], false, true": { "content": [ @@ -328,17 +328,17 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] }, "test.snf" ], + "timestamp": "2026-08-23T19:29:34.678862", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:21.571097723" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "homo_sapiens - [bam, bai], fasta, [], true, true": { "content": [ @@ -347,7 +347,7 @@ [ "SNIFFLES", "sniffles", - "2.7.3" + "2.8.0" ] ] }, @@ -355,7 +355,7 @@ "test.vcf.gz.tbi", [ "##fileformat=VCFv4.2", - "##source=Sniffles2_2.7.3" + "##source=Sniffles2_2.8.0" ], [ "##ALT=", @@ -394,6 +394,9 @@ "##FILTER=", "##FILTER=", "##FILTER=", + "##FILTER=", + "##FILTER=", + "##FILTER=", "##INFO=", "##INFO=", "##INFO=", @@ -413,16 +416,13 @@ "##INFO=", "##INFO=", "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=", - "##INFO=" + "##INFO=" ] ], + "timestamp": "2026-08-23T19:29:45.050345", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-20T09:48:30.406264548" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file