Merge branch 'master' into wipertools

nf-core · Dec 13, 2024 · 8caaa6e · 8caaa6e
2 parents 9c22c75 + 439f056
commit 8caaa6e
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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/modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/busco/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::busco=5.7.1
+  - bioconda::busco=5.8.2
diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
@@ -4,14 +4,14 @@ process BUSCO_BUSCO {
 
     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:
     tuple val(meta), path(fasta, stageAs:'tmp_input/*')
     val mode                              // Required:    One of genome, proteins, or transcriptome
-    val lineage                           // Required:    lineage to check against, "auto" enables --auto-lineage instead
-    path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
+    val lineage                           // Required:    lineage for checking against, or "auto/auto_prok/auto_euk" for enabling auto-lineage
+    path busco_lineages_path              // Recommended: busco lineages file - downloads if not set
     path config_file                      // Optional:    busco configuration file
 
     output:
@@ -21,7 +21,7 @@ process BUSCO_BUSCO {
     tuple val(meta), path("*-busco/*/run_*/full_table.tsv")           , emit: full_table            , optional: true
     tuple val(meta), path("*-busco/*/run_*/missing_busco_list.tsv")   , emit: missing_busco_list    , optional: true
     tuple val(meta), path("*-busco/*/run_*/single_copy_proteins.faa") , emit: single_copy_proteins  , optional: true
-    tuple val(meta), path("*-busco/*/run_*/busco_sequences")          , emit: seq_dir
+    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
     path "versions.yml"                                               , emit: versions
@@ -35,8 +35,10 @@ process BUSCO_BUSCO {
     }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
-    def busco_config = config_file ? "--config $config_file" : ''
-    def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
+    def busco_config = config_file ? "--config ${config_file}" : ''
+    def busco_lineage = lineage in [ 'auto', 'auto_prok', 'auto_euk']
+        ? lineage.replaceFirst('auto', '--auto-lineage').replaceAll('_', '-')
+        : "--lineage_dataset ${lineage}"
     def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
     """
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)

diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml
@@ -32,7 +32,8 @@ input:
         pattern: "{genome,proteins,transcriptome}"
   - - lineage:
         type: string
-        description: The BUSCO lineage to use, or "auto" to automatically select lineage
+        description: The BUSCO lineage to use, or "auto", "auto_prok" or "auto_euk"
+          to automatically select lineage
   - - busco_lineages_path:
         type: directory
         description: Path to local BUSCO lineages directory.

diff --git a/modules/nf-core/busco/busco/tests/main.nf.test b/modules/nf-core/busco/busco/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
                 ]
                 input[1] = 'genome'
-                input[2] = 'bacteria_odb10' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
+                input[2] = 'bacteria_odb12' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
                 input[3] = [] // Download busco lineage
                 input[4] = [] // No config
                 """
@@ -85,7 +85,7 @@ nextflow_process {
                     ]
                 ]
                 input[1] = 'genome'
-                input[2] = 'bacteria_odb10'
+                input[2] = 'bacteria_odb12'
                 input[3] = []
                 input[4] = []
                 """
@@ -126,7 +126,6 @@ nextflow_process {
             }
 
             assert snapshot(
-                    process.out.batch_summary[0][1],
                     process.out.full_table[0][1],
                     process.out.missing_busco_list[0][1],
                     process.out.versions[0]
@@ -274,7 +273,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
                 ]
                 input[1] = 'proteins'
-                input[2] = 'bacteria_odb10'
+                input[2] = 'bacteria_odb12'
                 input[3] = []
                 input[4] = []
                 """
@@ -336,7 +335,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
                 ]
                 input[1] = 'transcriptome'
-                input[2] = 'bacteria_odb10'
+                input[2] = 'bacteria_odb12'
                 input[3] = []
                 input[4] = []
                 """
@@ -397,7 +396,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
                 ]
                 input[1] = 'genome'
-                input[2] = 'bacteria_odb10'
+                input[2] = 'bacteria_odb12'
                 input[3] = []
                 input[4] = []
                 """
@@ -412,4 +411,4 @@ nextflow_process {
         }
     }
 
-}
+}
diff --git a/modules/nf-core/busco/busco/tests/main.nf.test.snap b/modules/nf-core/busco/busco/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+                    "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
                 ],
                 "batch_summary": [
                     [
                         {
                             "id": "test"
                         },
-                        "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "busco_dir": [
@@ -110,121 +110,141 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+                    "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:28:04.451297"
+        "timestamp": "2024-12-11T12:45:52.045550047"
     },
     "test_busco_eukaryote_augustus": {
         "content": [
             "test-eukaryota_odb10-busco.batch_summary.txt:md5,3ea3bdc423a461dae514d816bdc61c89",
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:26:36.974986"
+        "timestamp": "2024-12-11T13:07:45.550722277"
     },
     "test_busco_genome_single_fasta": {
         "content": [
-            "test-bacteria_odb10-busco.batch_summary.txt:md5,21b3fb771cf36be917cc451540d999be",
-            "full_table.tsv:md5,638fe7590f442c57361554dae330eca1",
-            "missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a",
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "test-bacteria_odb12-busco.batch_summary.txt:md5,e3e503e1540b633d95c273c465945740",
+            "full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7",
+            "missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0",
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:22:45.07816"
+        "timestamp": "2024-12-11T12:43:40.359736221"
     },
     "test_busco_genome_multi_fasta": {
         "content": [
-            "test-bacteria_odb10-busco.batch_summary.txt:md5,fcd3c208913e8abda3d6742c43fec5fa",
             [
-                "full_table.tsv:md5,c657edcc7d0de0175869717551df6e83",
-                "full_table.tsv:md5,638fe7590f442c57361554dae330eca1"
+                "full_table.tsv:md5,5e7df014f2804789f0d98ae2e09734ad",
+                "full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7"
             ],
             [
-                "missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112",
-                "missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a"
+                "missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50",
+                "missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0"
             ],
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:23:50.255602"
+        "timestamp": "2024-12-11T17:17:42.175675858"
     },
     "test_busco_eukaryote_metaeuk": {
         "content": [
             "test-eukaryota_odb10-busco.batch_summary.txt:md5,ff6d8277e452a83ce9456bbee666feb6",
-            "full_table.tsv:md5,92b1b1d5cb5ea0e2093d16f00187e8c7",
-            "missing_busco_list.tsv:md5,0352e563de290bf804c708323c35a9e3",
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "full_table.tsv:md5,9bfa9ef7d54ca6ad8bcf8e87729720b1",
+            "missing_busco_list.tsv:md5,325b529e5a8af2a392d747b4eddc150c",
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:25:38.159041"
+        "timestamp": "2024-12-11T13:07:17.335085326"
     },
     "test_busco_transcriptome": {
         "content": [
-            "test-bacteria_odb10-busco.batch_summary.txt:md5,8734b3f379c4c0928e5dd4ea1873dc64",
-            "full_table.tsv:md5,1b2ce808fdafa744c56b5f781551272d",
-            "missing_busco_list.tsv:md5,a6931b6470262b997b8b99ea0f1d14a4",
+            "test-bacteria_odb12-busco.batch_summary.txt:md5,6cd69d8a66b5f8b7fd4a9de758e7a739",
+            "full_table.tsv:md5,73a3a90c2fa8fef41cafed5a607fab66",
+            "missing_busco_list.tsv:md5,4778855c345f4e409750c9bbd38c5a0c",
             [
-                "1024388at2.faa:md5,797d603d262a6595a112e25b73e878b0",
-                "1054741at2.faa:md5,cd4b928cba6b19b4437746ba507e7195",
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+                "9809084at2.faa:md5,37e6214b4204dc31858e2ef2bad5db4a",
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+                "9809796at2.faa:md5,857aac8a22c00472bfc9add7fde94c5c",
+                "9810191at2.faa:md5,72b63933bb045b680e0635eb03915cc0",
+                "9811804at2.faa:md5,da341c24e763a949d16432bb052af321",
+                "9812272at2.faa:md5,7a54f872dd8243c6814852d40cf1bfc0",
+                "9812943at2.faa:md5,149da17f067cdce328a73f6364a95b26",
+                "9813375at2.faa:md5,49835b9f3188434c771a840b628b07f6",
+                "9814755at2.faa:md5,9b4c4648d250c2e6d04acb78f9cf6df0"
             ],
-            "single_copy_proteins.faa:md5,73e2c5d6a9b0f01f2deea3cc5f21b764",
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "single_copy_proteins.faa:md5,14124def13668c6d9b0d589207754b31",
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:27:53.992893"
+        "timestamp": "2024-12-11T12:45:43.336777509"
     },
     "test_busco_protein": {
         "content": [
-            "test-bacteria_odb10-busco.batch_summary.txt:md5,f5a782378f9f94a748aa907381fdef91",
-            "full_table.tsv:md5,812ab6a0496fccab774643cf40c4f2a8",
-            "missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112",
-            "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
+            "test-bacteria_odb12-busco.batch_summary.txt:md5,44d4cdebd61a3c8e8981ddf1829f83b3",
+            "full_table.tsv:md5,696bae3f377fd5dbaf19f1c522088d93",
+            "missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50",
+            "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T13:27:12.724862"
+        "timestamp": "2024-12-11T12:45:16.960592213"
     }
 }