Rename output file (#58)

* Rename output file * Add output rename in workflow * Update Cicero.sh
stjude · Apr 28, 2021 · f3a022c · f3a022c
1 parent 920cd51
commit f3a022c
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Showing 3 changed files with 15 additions and 4 deletions.
diff --git a/cgc/cicero.cwl b/cgc/cicero.cwl
@@ -86,12 +86,15 @@ outputs:
     type: File?
     outputBinding:
       glob: >-
-        $(inputs.bam_file.nameroot)/CICERO_DATADIR/$(inputs.bam_file.nameroot)/final_fusions.txt
+        $(inputs.bam_file.nameroot)/CICERO_DATADIR/$(inputs.bam_file.nameroot)/$(inputs.bam_file.nameroot).final_fusions.txt
 label: cicero
 arguments:
   - position: 101
     prefix: '-o'
-    valueFrom: (inputs.bam_file.nameroot)
+    valueFrom: $(inputs.bam_file.nameroot)
+  - position: 102
+    prefix: '-f'
+    valueFrom: $(inputs.bam_file.nameroot).final_fusions.txt
 requirements:
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement

diff --git a/cgc/rnapeg_cicero.cwl b/cgc/rnapeg_cicero.cwl
@@ -231,7 +231,7 @@
                         "id": "output_file",
                         "type": "File",
                         "outputBinding": {
-                            "glob": "$(inputs.bam_file.nameroot)/CICERO_DATADIR/$(inputs.bam_file.nameroot)/final_fusions.txt"
+                            "glob": "$(inputs.bam_file.nameroot)/CICERO_DATADIR/$(inputs.bam_file.nameroot)/$(inputs.bam_file.nameroot).final_fusions.txt"
                         }
                     }
                 ],
@@ -242,6 +242,12 @@
                         "shellQuote": false,
                         "position": 101,
                         "valueFrom": "$(inputs.bam_file.nameroot)"
+                    },
+                    {
+                        "prefix": "-f",
+                        "shellQuote": false,
+                        "position": 102,
+                        "valueFrom": "$(inputs.bam_file.nameroot).final_fusions.txt"
                     }
                 ],
                 "requirements": [

diff --git a/src/scripts/Cicero.sh b/src/scripts/Cicero.sh
@@ -352,6 +352,7 @@ echo "Step 05 - $(date +'%Y.%m.%d %H:%M:%S') - Filter"
 {
 cicero_filter.sh $CICERO_DATADIR $SAMPLE $GENOME
 cp $CICERO_DATADIR/$SAMPLE/final_fusions.txt $CICERO_DATADIR/$SAMPLE/final_fusions.report.html
+cp $CICERO_DATADIR/$SAMPLE/final_fusions.txt $CICERO_DATADIR/$SAMPLE/${SAMPLE}.final_fusions.txt
 } 1> 05_Filter.out 2> 05_Filter.err
 
 ## QC
@@ -364,7 +365,8 @@ fi
 ### STEP 06 - Rename output ###
 ###############################
 if [[ -n $FILENAME ]]; then
-    mv $OUTDIR/$CICERO_DATADIR/$SAMPLE/final_fusions.txt $OUTDIR/$CICERO_DATADIR/$SAMPLE/$FILENAME
+    echo "Renaming output file: $CICERO_DATADIR/$SAMPLE/final_fusions.txt $CICERO_DATADIR/$SAMPLE/$FILENAME" 2>&1
+    cp $CICERO_DATADIR/$SAMPLE/final_fusions.txt $CICERO_DATADIR/$SAMPLE/$FILENAME
 fi
 
 ############################