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Maxime Borry
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Merge branch 'master' of github.com:nf-core/modules into ribodetector
2 parents ccfdc1a + d855e94 commit 6ccf8e1

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‎.github/workflows/lint.yml‎

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NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
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NXF_VER: "24.10.1"
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NXF_VER: "25.04.8"
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jobs:
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pre-commit:

‎.github/workflows/nf-test-gpu.yml‎

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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NXF_ANSI_LOG: false
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NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
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NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
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# renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
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NXF_VER: "25.04.0"
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NXF_VER: "25.04.8"
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nf-test-changes:

‎.github/workflows/nf-test.yml‎

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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NXF_ANSI_LOG: false
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NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
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NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
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# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
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NXF_VER: "25.04.0"
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NXF_VER: "25.04.8"
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nf-test-changes:

‎.github/workflows/update-gpu-snapshot.yml‎

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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NXF_ANSI_LOG: false
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# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
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NXF_VER: "24.10.2"
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NXF_VER: "25.04.8"
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update-gpu-snapshot:

‎.github/workflows/update-sentieon-snapshot.yml‎

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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NXF_ANSI_LOG: false
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# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
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NXF_VER: "24.10.2"
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NXF_VER: "25.04.8"
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update-sentieon-snapshot:

‎.github/workflows/wave.yml‎

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# renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
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WAVE_VERSION: "1.5.0"
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# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
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NXF_VER: "24.10.1"
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NXF_VER: "25.04.8"
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generate-matrix:

‎modules/nf-core/agat/convertbed2gff/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::agat=1.4.2
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- "bioconda::agat=1.5.1"

‎modules/nf-core/agat/convertbed2gff/main.nf‎

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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/agat:1.4.2--pl5321hdfd78af_0' :
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'biocontainers/agat:1.4.2--pl5321hdfd78af_0' }"
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/033434db0bd6ba28660401e1059286f36641fd8ce55faa11973fe5eaf312adcd/data' :
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'community.wave.seqera.io/library/agat:1.5.1--ae3cd948ce5e9795' }"
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tuple val(meta), path(bed)

‎modules/nf-core/agat/convertbed2gff/tests/main.nf.test.snap‎

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]
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],
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"1": [
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"versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
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"versions.yml:md5,784d668bd6234b6376cc66f582ef6500"
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],
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"gff": [
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[
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]
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],
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"versions": [
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"versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
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"versions.yml:md5,784d668bd6234b6376cc66f582ef6500"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.10.3"
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"nf-test": "0.9.3",
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"nextflow": "25.04.8"
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},
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"timestamp": "2025-01-15T14:02:09.48826"
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"timestamp": "2025-10-17T11:12:31.27624"
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},
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"sarscov2 - bed12": {
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"content": [
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]
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],
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"1": [
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"versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
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"versions.yml:md5,784d668bd6234b6376cc66f582ef6500"
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],
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"gff": [
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[
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]
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],
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"versions": [
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"versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
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"versions.yml:md5,784d668bd6234b6376cc66f582ef6500"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.10.3"
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"nf-test": "0.9.3",
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"nextflow": "25.04.8"
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},
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"timestamp": "2025-01-15T14:02:03.549345"
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"timestamp": "2025-10-17T11:12:25.691233"
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}
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}

‎modules/nf-core/agat/convertspgff2gtf/environment.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::agat=1.4.2
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- "bioconda::agat=1.5.1"

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