busco updated/patched/tested

sanger-tol · Dec 2, 2024 · bfe9445 · bfe9445
1 parent e11951c
commit bfe9445
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Showing 15 changed files with 1,515 additions and 138 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -49,14 +49,14 @@ process {
         ]
     }
 
-    withName: BUSCO {
+    withName: "BUSCO|BUSCO_BUSCO" {
         // Obey "use_work_dir_as_temp", except for large genomes
         scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         ext.args = { 'test' in workflow.profile.tokenize(',') ?
                         // Additional configuration to speed processes up during testing.
                         // Note: BUSCO *must* see the double-quotes around the parameters
-                        '--mode genome --tar --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
-                    : '--mode genome --tar' }
+                        '--mode genome --tar --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
+                    : '--mode genome --tar --metaeuk ' }
     }
 
     withName: "RESTRUCTUREBUSCODIR" {

diff --git a/modules.json b/modules.json
@@ -8,68 +8,92 @@
                     "bedtools/bamtobed": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
-                    "busco": {
+                    "busco/busco": {
                         "branch": "master",
-                        "git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/busco/busco.diff"
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ],
+                        "patch": "modules/nf-core/busco/busco/busco-busco.diff"
                     },
                     "cooler/cload": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cooler/dump": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastk/fastk": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
                     },
                     "gnu/sort": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/nf-core/busco/busco.diff → modules/nf-core/busco/busco/busco-busco.diff b/modules/nf-core/busco/busco.diff → modules/nf-core/busco/busco/busco-busco.diff
diff --git a/modules/nf-core/busco/environment.yml → modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/environment.yml → modules/nf-core/busco/busco/environment.yml
diff --git a/modules/nf-core/busco/main.nf → modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/main.nf → modules/nf-core/busco/busco/main.nf
diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml