complete script for qualimap

src/qualimap/qualimap_rnaseq/config.vsh.yaml

@@ -21,32 +21,22 @@ argument_groups:
 
 - name: "Output"
   arguments: 
-  - name: "--output_dir"
+  - name: "--output"
     direction: output
     type: file
-    required: false
-    default: $id.qualimap_output
-    description: path to output directory for raw data and report.
-  - name: "--output_pdf"
-    type: file
-    direction: output
-    required: false
-    must_exist: false
-    default: $id.report.pdf
-    description: path to output file for pdf report.
-  - name: "--output_format"
-    type: string
-    required: false
-    default: html
-    description: Format of the output report (PDF or HTML, default is HTML)
+    required: true
+    example: rnaseq_qc_results.txt
+    description: Text file containing the RNAseq QC results.
   - name: "--output_counts"
     type: file
     required: false
-    description: Output file for computed counts. If only name of the file is provided, then the file will be saved in the output folder.
-  - name: "--output_file"
+    direction: output
+    description: Output file for computed counts.
+  - name: "--output_report"
     type: file
+    direction: output
     required: false
-    description: Output file for PDF report (default value is report.pdf).
+    description: PDF report output file.
 
 - name: "Optional"
   arguments: 
@@ -86,6 +76,7 @@ argument_groups:
     default: 4G 
     description: maximum Java heap memory size, default = 4G.
 
+
 resources:
   - type: bash_script
     path: script.sh

src/qualimap/qualimap_rnaseq/script.sh

@@ -1,22 +1,37 @@
 #!/bin/bash
 
-sleep 10000
-
 set -eo pipefail
 
-mkdir -p $par_output_dir
+tmp_dir=$(mktemp -d -p "$meta_temp_dir" qualimap_XXXXXXXXX)
+
+
+if [ -n "$par_output_file" ]; then
+    outfile=$(basename "$par_output_file")
+fi
+
+if [ -n "$par_output_counts" ]; then
+    counts=$(basename "$par_output_counts")
+fi
 
 qualimap rnaseq \
-    # --algorithm=$par_algorithm \
     --java-mem-size=$par_java_memory_size \
+    --algorithm $par_algorithm \
     --num-pr-bases $par_pr_bases \
     --num-tr-bias $par_tr_bias \
     --sequencing-protocol $par_sequencing_protocol \
     -bam $par_input \
     -gtf $par_gtf \
-    ${par_paired:+-pe} \
-    ${par_sorted:+-s} \
-    -outdir $par_output_dir \
-    # -oc $par_output_counts \
-    # -outfile $par_output_file \
-    -outformat $par_output_format 
+    -outdir "$tmp_dir" \
+    -outformat pdf \
+    ${par_output_file:+-outfile "$outfile"} \
+    ${par_output_counts:+-oc "$counts"}
+
+mv "$tmp_dir/rnaseq_qc_results.txt" "$par_output"
+
+if [ -n "$par_output_file" ]; then
+    mv "$tmp_dir/$outfile" "$par_output_file"
+fi
+
+if [ -n "$par_output_counts" ]; then
+    mv "$tmp_dir/$counts" "$par_output_counts"
+fi