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nf-core · Dec 17, 2024 · 50e2138 · 50e2138
2 parents 75a029c + 2efd1bc
commit 50e2138
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diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
@@ -183,6 +183,8 @@ exclude:
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
   - profile: conda
+    path: modules/nf-core/parabricks/mutectcaller
+ - profile: conda
     path: modules/nf-core/parabricks/dbsnp
   - profile: conda
     path: modules/nf-core/parabricks/indexgvcf

diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -74,14 +74,14 @@ jobs:
 
   nf-test-gpu:
     runs-on: "gpu"
-    name: "GPU | ${{ matrix.profile }} | ${{ matrix.shard }}"
+    name: "GPU Test | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: nf-test-changes
     if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }}
     strategy:
       fail-fast: false
       matrix:
         shard: [1, 2]
-        profile: [docker_self_hosted, singularity] # conda?
+        profile: [docker_self_hosted, singularity]
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: 2

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -76,7 +76,7 @@ jobs:
           echo ${{ steps.outputs.outputs.subworkflows }}
   nf-test:
     runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
-    name: "${{ matrix.profile }} | ${{ matrix.shard }}"
+    name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: nf-test-changes
     if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }}
     strategy:

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   pytest-changes:
@@ -278,20 +278,13 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Set up miniconda
+      - name: Conda setup
+        if: matrix.profile == 'conda'
         uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
         with:
-          miniconda-version: "latest"
-          channels: conda-forge,bioconda
-          python-version: "3.11"
-
-      - name: Conda setup
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
+          auto-update-conda: true
+          conda-solver: libmamba
+          conda-remove-defaults: true
 
       # Test the module
       - name: Run pytest-workflow

diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
@@ -24,6 +24,8 @@ process BUSCO_BUSCO {
     tuple val(meta), path("*-busco/*/run_*/busco_sequences")          , emit: seq_dir               , optional: true
     tuple val(meta), path("*-busco/*/translated_proteins")            , emit: translated_dir        , optional: true
     tuple val(meta), path("*-busco")                                  , emit: busco_dir
+    tuple val(meta), path("busco_downloads/lineages/*")               , emit: downloaded_lineages   , optional: true
+
     path "versions.yml"                                               , emit: versions
 
     when:

diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml
@@ -46,7 +46,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco.batch_summary.txt":
           type: file
           description: Summary of all sequence files analyzed
@@ -56,7 +56,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - short_summary.*.txt:
           type: file
           description: Short Busco summary in plain text format
@@ -66,7 +66,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - short_summary.*.json:
           type: file
           description: Short Busco summary in JSON format
@@ -76,7 +76,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco/*/run_*/full_table.tsv":
           type: file
           description: Full BUSCO results table
@@ -86,7 +86,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco/*/run_*/missing_busco_list.tsv":
           type: file
           description: List of missing BUSCOs
@@ -96,7 +96,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco/*/run_*/single_copy_proteins.faa":
           type: file
           description: Fasta file of single copy proteins (transcriptome mode)
@@ -106,7 +106,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco/*/run_*/busco_sequences":
           type: directory
           description: BUSCO sequence directory
@@ -116,7 +116,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco/*/translated_proteins":
           type: directory
           description: Six frame translations of each transcript made by the transcriptome
@@ -127,11 +127,21 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*-busco":
           type: directory
           description: BUSCO lineage specific output
           pattern: "*-busco"
+  - downloaded_lineages:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "busco_downloads/lineages/*":
+          type: directory
+          description: Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12
+          pattern: "busco_downloads/lineages/*"
   - versions:
       - versions.yml:
           type: file

diff --git a/modules/nf-core/busco/busco/tests/main.nf.test b/modules/nf-core/busco/busco/tests/main.nf.test
@@ -406,7 +406,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.batch_summary,
+                    process.out.versions
+                ).match() }
             )
         }
     }

diff --git a/modules/nf-core/busco/busco/tests/main.nf.test.snap b/modules/nf-core/busco/busco/tests/main.nf.test.snap
@@ -1,124 +1,23 @@
 {
     "minimal-stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-
-                ],
-                "2": [
-
-                ],
-                "3": [
-
-                ],
-                "4": [
-
-                ],
-                "5": [
-
-                ],
-                "6": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-
-                        ]
-                    ]
-                ],
-                "7": [
-
-                ],
-                "8": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            [
-                                [
-                                    [
-
-                                    ]
-                                ]
-                            ]
-                        ]
-                    ]
-                ],
-                "9": [
-                    "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
-                ],
-                "batch_summary": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "busco_dir": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            [
-                                [
-                                    [
-
-                                    ]
-                                ]
-                            ]
-                        ]
-                    ]
-                ],
-                "full_table": [
-
-                ],
-                "missing_busco_list": [
-
-                ],
-                "seq_dir": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-
-                        ]
-                    ]
-                ],
-                "short_summaries_json": [
-
-                ],
-                "short_summaries_txt": [
-
-                ],
-                "single_copy_proteins": [
-
-                ],
-                "translated_dir": [
-
-                ],
-                "versions": [
-                    "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
-            }
+            ],
+            [
+                "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T12:45:52.045550047"
+        "timestamp": "2024-12-13T15:30:45.505241761"
     },
     "test_busco_eukaryote_augustus": {
         "content": [

diff --git a/modules/nf-core/busco/generateplot/environment.yml b/modules/nf-core/busco/generateplot/environment.yml
@@ -1,7 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::busco=5.7.1
+  - bioconda::busco=5.8.2
diff --git a/modules/nf-core/busco/generateplot/main.nf b/modules/nf-core/busco/generateplot/main.nf
@@ -3,8 +3,8 @@ process BUSCO_GENERATEPLOT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
-        'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0':
+        'biocontainers/busco:5.8.2--pyhdfd78af_0' }"
 
     input:
     path short_summary_txt, stageAs: 'busco/*'

diff --git a/modules/nf-core/busco/generateplot/tests/main.nf.test.snap b/modules/nf-core/busco/generateplot/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T15:40:01.523993"
+        "timestamp": "2024-12-12T17:44:49.021631034"
     },
     "stub": {
         "content": [
@@ -18,20 +18,20 @@
                     "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "1": [
-                    "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                    "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
                 ],
                 "png": [
                     "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                    "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T15:40:11.864276"
+        "timestamp": "2024-12-12T17:44:57.632273743"
     }
 }
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
@@ -3,3 +3,8 @@ channels:
   - bioconda
 dependencies:
   - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34