Improved properties descriptions in schema and README.md

nf-core · Oct 29, 2024 · d4a97e9 · d4a97e9
1 parent 6389825
commit d4a97e9
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -52,7 +52,7 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/fastqrepair \
-   -profile <test/docker> \
+   -profile <test/docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
 ```

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -38,7 +41,10 @@
                 },
                 "qin": {
                     "type": "integer",
-                    "enum": [33, 64],
+                    "enum": [
+                        33,
+                        64
+                    ],
                     "default": 33,
                     "description": "the ASCII offset (33=Sanger, 64=old Solexa).",
                     "fa_icon": "fas fa-puzzle-piece"
@@ -47,6 +53,7 @@
                     "type": "string",
                     "default": "ACGTN",
                     "description": "Allowed character in the SEQ line.",
+                    "help_text": "SEQ lines containing characters not listed here will be discarded",
                     "fa_icon": "fas fa-solid fa-arrows-left-right-to-line"
                 },
                 "email": {
@@ -125,11 +132,19 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "publish_dir_all_tools": {
                     "type": "boolean",
+                    "default": false,
                     "description": "To specify whether to publish all pipeline intermediate results to output directory.",
                     "help_text": "This option tells the pipeline whether to publish all intermediate results to output directory.",
                     "fa_icon": "fas fa-copy",