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Merge pull request #355 from jonasscheid/merge-template-402
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‎CHANGELOG.md‎

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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `bcftools` | 1.21 | 1.22 |
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| `multiqc` | 1.32 | 1.34 |
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| `bcftools` | 1.21 | 1.23.1 |
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| `multiqc` | 1.32 | 1.35 |
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| `snpsift` | 4.3 | 5.4c |
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| `nf-core` | 3.4.1 | 4.0.2 |
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### `Changed`
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- [#320](https://github.com/nf-core/epitopeprediction/pull/320) Set default genome reference to GRCh38 ([@jonasscheid](https://github.com/jonasscheid/)).
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- Remove `--ensembl_dataset` parameter; Ensembl dataset is now auto-detected from `--genome_reference` (supports human and mouse genomes, or direct Ensembl URL).
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- [#336](https://github.com/nf-core/epitopeprediction/pull/336) Added NetMHCpan 4.2 mode config file instructions to the nf-core usage documentation. ([@Kabooni](https://github.com/Kabooni)).
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- [#346](https://github.com/nf-core/epitopeprediction/issues/346) Replace `CAT_CAT` with `FIND_CONCATENATE` to fix output filename collisions ([@jonasscheid](https://github.com/jonasscheid/)).
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- Bump nf-core modules and subworkflows to latest ([@jonasscheid](https://github.com/jonasscheid/)).
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## 3.1.0 - Lustnau - 2025-10-22
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‎conf/containers_conda_lock_files_amd64.config‎

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process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
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process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }

‎conf/containers_conda_lock_files_arm64.config‎

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process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
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process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }

‎conf/containers_docker_amd64.config‎

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process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
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process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042' } }

‎conf/containers_docker_arm64.config‎

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process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
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process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4' } }

‎conf/containers_singularity_https_amd64.config‎

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process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
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process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data' } }

‎conf/containers_singularity_https_arm64.config‎

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process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
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process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data' } }

‎conf/containers_singularity_oras_amd64.config‎

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process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
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process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393' } }

‎conf/containers_singularity_oras_arm64.config‎

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process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
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process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0' } }

‎modules.json‎

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"nf-core": {
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"bcftools/norm": {
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"branch": "master",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"bcftools/stats": {
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"branch": "master",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"cat/cat": {
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"find/concatenate": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
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"git_sha": "cd0ad387832473916b1f1c80c2ca673a7883bf94",
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"installed_by": ["modules"]
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},
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"snpsift/split": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "9091c30765ad62592d9a3b07f811d5eec142e471",
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"installed_by": ["modules"]
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}
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}
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"nf-core": {
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"utils_nextflow_pipeline": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
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"installed_by": ["subworkflows"]
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},
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"utils_nfcore_pipeline": {
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},
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"utils_nfschema_plugin": {
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"branch": "master",
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"git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
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"git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
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"installed_by": ["subworkflows"]
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}
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}

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