add missing versions, fix linting warning

nf-core · May 28, 2024 · 3949496 · 3949496
1 parent cf6a8a5
commit 3949496
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Showing 5 changed files with 37 additions and 11 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,2 +1,4 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  files_exist:  conf/igenomes.config
diff --git a/docs/usage.md b/docs/usage.md
@@ -25,13 +25,15 @@ A final samplesheet file may look something like the one below:
 ```csv title="samplesheet.csv"
 id,query
 BicD2,Q8TD16
+HBB,P68871
 ```
 
 or the one below, if you provide the sequence of the protein in FASTA format:
 
 ```csv title="samplesheet.csv"
 id,fasta
 BicD2,/home/myuser/data/bicd2.fa
+HBB,/home/myuser/data/hbb.fa
 ```
 
 | Column  | Description                                                                                                                                       |

diff --git a/modules.json b/modules.json
@@ -8,37 +8,51 @@
                     "csvtk/concat": {
                         "branch": "master",
                         "git_sha": "cfe2a24902bfdfe8132f11461ffda92d257f9f09",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "csvtk/join": {
                         "branch": "master",
                         "git_sha": "5e0c5677ea33b3d4c3793244035a191bd03e6736",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastme": {
                         "branch": "master",
                         "git_sha": "5f4e755fdc22c6e40d740ab27ea9b1004e806cb5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "iqtree": {
                         "branch": "master",
                         "git_sha": "ba03053ffa300ccdd044545131ba033b73f327fe",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tcoffee/align": {
                         "branch": "master",
                         "git_sha": "5c82ca0a942f2793859bb2f25601eb69c50590dc",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -47,20 +61,26 @@
                     "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/modules/local/create_tcoffeetemplate.nf b/modules/local/create_tcoffeetemplate.nf
@@ -11,6 +11,7 @@ process CREATE_TCOFFEETEMPLATE {
 
     output:
     tuple val (meta), path("*_template.txt"), emit: template
+    path("versions.yml"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/dump_params.nf b/modules/local/dump_params.nf
@@ -17,6 +17,7 @@ process DUMP_PARAMS {
 
     output:
     tuple val(meta), path("params.yml"), emit: params
+    path("versions.yml"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ process CREATE_TCOFFEETEMPLATE { @@
         output:
         tuple val (meta), path("*_template.txt"), emit: template
+        path("versions.yml"), emit: versions
         when:
         task.ext.when == null || task.ext.when
@@ Expand Down @@