Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison…

… into dev
oist · May 24, 2024 · ef7d436 · ef7d436
2 parents a3fef68 + aed4dff
commit ef7d436
Show file tree

Hide file tree

Showing 3 changed files with 42 additions and 19 deletions.
diff --git a/modules.json b/modules.json
@@ -8,47 +8,65 @@
                     "assemblyscan": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gfastats": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/dotplot": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/lastal": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/lastdb": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/mafswap": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/split": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "last/train": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -57,20 +75,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -64,8 +64,8 @@ params {
     m2m                        = false
 
     // Alignment options
-    lastal_args                = 'C2'
-    lastal_extr_args           = 'D1e9'
+    lastal_args                = '-C2 -D1e9'
+    lastal_extr_args           = ''
     last_split_mismap          = '1e-05'
     lastal_params              = null
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -369,13 +369,12 @@
             "properties": {
                 "lastal_args": {
                     "type": "string",
-                    "default": "C2",
-                    "description": "this defaults to -C2 and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial."
+                    "default": "-C2 -D1e9",
+                    "description": "this defaults to -C2 -D1e9)and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial."
                 },
                 "lastal_extr_args": {
                     "type": "string",
-                    "default": "D1e9",
-                    "description": "(default: -D1e9) is only passed to lastal and can be used for arguments that are not recognised by last-train."
+                    "description": "(default: ' ' is only passed to lastal and can be used for arguments that are not recognised by last-train."
                 },
                 "last_split_mismap": {
                     "type": "string",