Merge branch 'dev' into fix/parquet-merge-predictions

Author: jonasscheid

CHANGELOG.md

@@ -27,18 +27,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Dependency  | Old version | New version |
 | ----------- | ----------- | ----------- |
 | `bcftools`  | 1.21        | 1.22        |
+| `mhcgnomes` | 1.8.6       | 3.32.0      |
 | `multiqc`   | 1.32        | 1.34        |
 | `nf-core`   | 3.4.1       | 4.0.2       |
-| `mhcgnomes` | 1.8.6       | 3.32.0      |
 | `pyarrow`   | -           | 24.0.0      |
+| `snpsift`   | 4.3         | 5.4c        |
+
 
 ### `Changed`
 
 - [#316](https://github.com/nf-core/epitopeprediction/pull/316) Added parameter `--biomart_dump` in `epaa.py` ([@SusiJo](https://github.com/SusiJo/)).
 - [#320](https://github.com/nf-core/epitopeprediction/pull/320) Set default genome reference to GRCh38 ([@jonasscheid](https://github.com/jonasscheid/)).
 - Remove `--ensembl_dataset` parameter; Ensembl dataset is now auto-detected from `--genome_reference` (supports human and mouse genomes, or direct Ensembl URL).
 - [#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)).
-- [#356](https://github.com/nf-core/epitopeprediction/pull/356) Switch `MERGE_PREDICTIONS` → `SUMMARIZE_RESULTS` intermediate from CSV to Parquet (zstd) and migrate `PREPARE_PREDICTION_INPUT`, `MERGE_PREDICTIONS`, and `SUMMARIZE_RESULTS` to a shared multi-arch Seqera Container (mhcgnomes 3.32.0 + pyarrow 24.0.0). Includes pandas 3 compatibility fixes in `summarize_results.py` and a defensive guard in `prepare_prediction_input.py` for mhcgnomes 3.x `AlleleWithoutGene` cases (closes [#343](https://github.com/nf-core/epitopeprediction/issues/343)) ([@jonasscheid](https://github.com/jonasscheid/))
+- [#356](https://github.com/nf-core/epitopeprediction/pull/356) Switch `MERGE_PREDICTIONS` → `SUMMARIZE_RESULTS` intermediate from CSV to Parquet and migrate `PREPARE_PREDICTION_INPUT`, `MERGE_PREDICTIONS`, and `SUMMARIZE_RESULTS` to a shared multi-arch Seqera Container ([@jonasscheid](https://github.com/jonasscheid/))
+- [#346](https://github.com/nf-core/epitopeprediction/issues/346) Replace `CAT_CAT` with `FIND_CONCATENATE`([@jonasscheid](https://github.com/jonasscheid/)).
+- Bump nf-core modules and subworkflows to latest ([@jonasscheid](https://github.com/jonasscheid/)).
 
 ## 3.1.0 - Lustnau - 2025-10-22
 

conf/containers_conda_lock_files_amd64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }

conf/containers_conda_lock_files_arm64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }

conf/containers_docker_amd64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042' } }

conf/containers_docker_arm64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4' } }

conf/containers_singularity_https_amd64.config

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

conf/containers_singularity_https_arm64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data' } }

conf/containers_singularity_oras_amd64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393' } }

conf/containers_singularity_oras_arm64.config

@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0' } }

modules.json

@@ -7,32 +7,32 @@
                 "nf-core": {
                     "bcftools/norm": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
-                    "cat/cat": {
+                    "find/concatenate": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
+                        "git_sha": "cd0ad387832473916b1f1c80c2ca673a7883bf94",
                         "installed_by": ["modules"]
                     },
                     "snpsift/split": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "9091c30765ad62592d9a3b07f811d5eec142e471",
                         "installed_by": ["modules"]
                     }
                 }
@@ -41,7 +41,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -51,7 +51,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
                         "installed_by": ["subworkflows"]
                     }
                 }