🧹 mislabeled inputs

kids-first · Sep 30, 2021 · fa5b10f · fa5b10f
1 parent 0f7dbc5
commit fa5b10f
Showing 1 changed file with 13 additions and 14 deletions.
diff --git a/workflows/kfdrc-cnvkit-wf.cwl b/workflows/kfdrc-cnvkit-wf.cwl
@@ -45,17 +45,16 @@ inputs:
   output_basename: {type: 'string', doc: "Basename to use for outputs"}
 
   # Batch
-  input_reads: {type: 'File[]', inputBinding: {position: 99}, secondaryFiles: [{pattern: ".bai",
-        required: false}, {pattern: "^.bai", required: false}, {pattern: ".crai",
-        required: false}, {pattern: "^.crai", required: false}], doc: "Mapped sequence\
-      \ reads in CRAM or BAM format", "sbg:fileTypes": "BAM, CRAM"}
-  input_normal_reads: {type: 'File[]?', inputBinding: {prefix: "--normal"}, secondaryFiles: [
-      {pattern: ".bai", required: false}, {pattern: "^.bai", required: false}, {pattern: ".crai",
-        required: false}, {pattern: "^.crai", required: false}], doc: "Normal samples\
-      \ (.bam/.cram) used to construct the pooled, paired, or flat reference. If this\
-      \ option is used but no filenames are given, a 'flat' reference will be built.\
-      \ Otherwise, all filenames following this option will be used.", "sbg:fileTypes": "BAM,\
-      \ CRAM"}
+  input_reads: {type: 'File[]', secondaryFiles: [{pattern: ".bai", required: false},
+      {pattern: "^.bai", required: false}, {pattern: ".crai", required: false}, {
+        pattern: "^.crai", required: false}], doc: "Mapped sequence reads in CRAM\
+      \ or BAM format", "sbg:fileTypes": "BAM, CRAM"}
+  input_normal_reads: {type: 'File[]?', secondaryFiles: [{pattern: ".bai", required: false},
+      {pattern: "^.bai", required: false}, {pattern: ".crai", required: false}, {
+        pattern: "^.crai", required: false}], doc: "Normal samples (.bam/.cram) used\
+      \ to construct the pooled, paired, or flat reference. If this option is used\
+      \ but no filenames are given, a 'flat' reference will be built. Otherwise, all\
+      \ filenames following this option will be used.", "sbg:fileTypes": "BAM, CRAM"}
   reference_fasta: {type: 'File?', secondaryFiles: [.fai], doc: "Reference genome,\
       \ FASTA format; needed if cnv kit cnn not already built", "sbg:suggestedValue": {
       class: File, path: 60639014357c3a53540ca7a3, name: Homo_sapiens_assembly38.fasta,
@@ -94,11 +93,11 @@ inputs:
       \ are approximate)."}
   antitarget_minimum_size: {type: 'int?', doc: "Minimum size of antitarget bins (smaller\
       \ regions are dropped)."}
-  cluster_plot: {type: 'boolean?', doc: "Calculate and use cluster-specific summary\
-      \ stats in the reference pool to normalize samples."}
+  cluster: {type: 'boolean?', doc: "Calculate and use cluster-specific summary stats\
+      \ in the reference pool to normalize samples."}
   scatter_plot: {type: 'boolean?', doc: "Create a whole-genome copy ratio profile\
       \ as a PDF scatter plot."}
-  diagram: {type: 'boolean?', doc: "Create an ideogram of copy ratios on chromosomes\
+  diagram_plot: {type: 'boolean?', doc: "Create an ideogram of copy ratios on chromosomes\
       \ as a PDF."}
 
   # Call