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Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
AlexsLemonade · Mar 7, 2024 · 353a171 · 353a171
1 parent c9cda49
commit 353a171
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/merge.nf b/merge.nf
@@ -22,7 +22,7 @@ if (!file(params.run_metafile).exists()) {
   param_error = true
 }
 
-if(param_error) {
+if (param_error) {
   System.exit(1)
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,7 @@
       "type": "object",
       "fa_icon": "fas fa-terminal",
       "description": "Define where the pipeline should find input data and save output data.",
-      "required": ["outdir", "run_metafile"],
+      "required": ["outdir", "run_metafile", "sample_metafile"],
       "properties": {
         "outdir": {
           "type": "string",
@@ -41,7 +41,7 @@
           "fa_icon": "fas fa-file-alt",
           "format": "file-path",
           "mimetype": "text/tab-separated-values",
-          "description": "A file containing information to map cellhash barcodes to samples.  See  https://github.com/AlexsLemonade/scpca-nf/blob/main/external-instructions.md#multiplexed-cellhash-libraries"
+          "description": "A file containing information to map cellhash barcodes to samples.  See https://github.com/AlexsLemonade/scpca-nf/blob/main/external-instructions.md#multiplexed-cellhash-libraries"
         },
         "results_dir": {
           "type": "string",
@@ -167,13 +167,13 @@
           "type": "string",
           "default": "s3://scpca-references/celltype/singler_models",
           "format": "directory-path",
-          "description": "Directory of singleR model files"
+          "description": "Directory of `SingleR` model files"
         },
         "cellassign_ref_dir": {
           "type": "string",
           "default": "s3://scpca-references/celltype/cellassign_references",
           "format": "directory-path",
-          "description": "Directory of CellAssign reference data"
+          "description": "Directory of `CellAssign` reference data"
         },
         "ref_metadata": {
           "type": "string",
@@ -193,7 +193,7 @@
           "type": "string",
           "default": "s3://scpca-references/celltype/singler_references",
           "format": "directory-path",
-          "description": "Directory of singleR reference files, used in `build-celltype-ref.nf`",
+          "description": "Directory of `SingleR` reference files, used in `build-celltype-ref.nf`",
           "hidden": true
         },
         "celltype_ref_metadata": {
@@ -238,7 +238,7 @@
         "prob_compromised_cutoff": {
           "type": "number",
           "default": 0.75,
-          "description": "Cutoff for MiQC to keep a cell"
+          "description": "Cutoff for `miQC` to keep a cell"
         },
         "gene_cutoff": {
           "type": "integer",
@@ -275,7 +275,7 @@
         "singler_label_name": {
           "type": "string",
           "default": "label.ont",
-          "description": "Label name for singleR references"
+          "description": "Label name for `SingleR` references"
         }
       }
     },