diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b000682..7529bb6e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,8 +29,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | -------- | ----------- | ----------- | | bcftools | 1.18 | 1.20 | +| genmod | 3.8.2 | 3.8.3 | | mosdepth | 0.3.6 | 0.3.8 | -| multiqc | 1.21 | 1.25 | +| multiqc | 1.21 | 1.25.1 | | picard | 3.1.1 | 3.2.0 | | samtools | 1.19.2 | 1.21 | | sentieon | 202308.02 | 202308.03 | diff --git a/modules.json b/modules.json index d2a9ebaf..a1cb2151 100644 --- a/modules.json +++ b/modules.json @@ -243,22 +243,22 @@ }, "genmod/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", "installed_by": ["modules"] }, "genmod/compound": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", "installed_by": ["modules"] }, "genmod/models": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", "installed_by": ["modules"] }, "genmod/score": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", "installed_by": ["modules"] }, "glnexus": { @@ -294,7 +294,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] }, "ngsbits/samplegender": { diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml index 1eca76fa..bbc3fd97 100644 --- a/modules/nf-core/genmod/annotate/environment.yml +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index eb161187..033caa9a 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -4,8 +4,8 @@ process GENMOD_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml index 1eca76fa..bbc3fd97 100644 --- a/modules/nf-core/genmod/compound/environment.yml +++ b/modules/nf-core/genmod/compound/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 1731b722..4831da85 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -4,8 +4,8 @@ process GENMOD_COMPOUND { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml index 1eca76fa..bbc3fd97 100644 --- a/modules/nf-core/genmod/models/environment.yml +++ b/modules/nf-core/genmod/models/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 0504574a..90c1fd48 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -4,8 +4,8 @@ process GENMOD_MODELS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml index 1eca76fa..bbc3fd97 100644 --- a/modules/nf-core/genmod/score/environment.yml +++ b/modules/nf-core/genmod/score/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 15be5f74..522e05b6 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -4,8 +4,8 @@ process GENMOD_SCORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b0..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebdb..9724d2f3 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e469..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file