address pr comments

src/qualimap/qualimap_rnaseq/config.vsh.yaml

@@ -65,13 +65,11 @@ argument_groups:
       type: string
       required: false
       choices: ["uniquely-mapped-reads", "proportional"]
-      default: uniquely-mapped-reads
       description: Counting algorithm (uniquely-mapped-reads (default) or proportional).
     - name: "--sequencing_protocol"
       type: string
       required: false
       choices: ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"]
-      default: non-strand-specific
       description: Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).
     - name: "--paired"
       type: boolean_true
@@ -82,7 +80,6 @@ argument_groups:
     - name: "--java_memory_size"
       type: string
       required: false
-      default: 4G 
       description: maximum Java heap memory size, default = 4G.
 
 resources:

src/qualimap/qualimap_rnaseq/script.sh

@@ -5,13 +5,13 @@ set -eo pipefail
 tmp_dir=$(mktemp -d -p "$meta_temp_dir" qualimap_XXXXXXXXX)
 
 # Handle output parameters
-if [ -n "$par_output_report" ]; then
-    outfile=$(basename "$par_output_report")
+if [ -n "$par_report" ]; then
+    outfile=$(basename "$par_report")
     report_extension="${outfile##*.}"
 fi
 
-if [ -n "$par_output_counts" ]; then
-    counts=$(basename "$par_output_counts")
+if [ -n "$par_counts" ]; then
+    counts=$(basename "$par_counts")
 fi
 
 # disable flags
@@ -28,23 +28,23 @@ qualimap rnaseq \
     -outdir "$tmp_dir" \
     ${par_num_pr_bases:+--num-pr-bases $par_num_pr_bases} \
     ${par_num_tr_bias:+--num-tr-bias $par_num_tr_bias} \
-    ${par_output_report:+-outformat $report_extension} \
+    ${par_report:+-outformat $report_extension} \
     ${par_paired:+--paired} \
     ${par_sorted:+--sorted} \
-    ${par_output_report:+-outfile "$outfile"} \
-    ${par_output_counts:+-oc "$counts"}
+    ${par_report:+-outfile "$outfile"} \
+    ${par_counts:+-oc "$counts"}
 
 # Move output files
-mv "$tmp_dir/rnaseq_qc_results.txt" "$par_output"
+mv "$tmp_dir/rnaseq_qc_results.txt" "$par_qc_results"
 
-if [ -n "$par_output_report" ] && [ $report_extension = "html" ]; then
-    mv "$tmp_dir/qualimapReport.html" "$par_output_report"
+if [ -n "$par_report" ] && [ $report_extension = "html" ]; then
+    mv "$tmp_dir/qualimapReport.html" "$par_report"
 fi
 
-if [ -n "$par_output_report" ] && [ $report_extension = "pdf" ]; then
-    mv "$tmp_dir/$outfile" "$par_output_report"
+if [ -n "$par_report" ] && [ $report_extension = "pdf" ]; then
+    mv "$tmp_dir/$outfile" "$par_report"
 fi
 
-if [ -n "$par_output_counts" ]; then
-    mv "$tmp_dir/$counts" "$par_output_counts"
+if [ -n "$par_counts" ]; then
+    mv "$tmp_dir/$counts" "$par_counts"
 fi

src/qualimap/qualimap_rnaseq/test.sh

@@ -27,9 +27,9 @@ echo "> Running qualimap with html output report"
 "$meta_executable" \
     --bam $test_dir/a.bam \
     --gtf $test_dir/annotation.gtf \
-    --output_report report.html \
-    --output_counts counts.txt \
-    --output output.txt
+    --report report.html \
+    --counts counts.txt \
+    --qc_results output.txt
 
 echo ">> Checking output"
 assert_file_exists "report.html"
@@ -71,9 +71,9 @@ echo "> Running qualimap with pdf output report"
 "$meta_executable" \
     --bam $test_dir/a.bam \
     --gtf $test_dir/annotation.gtf \
-    --output_report report.pdf \
-    --output_counts counts.txt \
-    --output output.txt
+    --report report.pdf \
+    --counts counts.txt \
+    --qc_results output.txt
 
 echo ">> Checking output"
 assert_file_exists "report.pdf"
@@ -97,7 +97,7 @@ echo "> Running qualimap without report and counts output"
 "$meta_executable" \
     --bam $test_dir/a.bam \
     --gtf $test_dir/annotation.gtf \
-    --output output.txt
+    --qc_results output.txt
 
 echo ">> Checking output"
 assert_file_doesnt_exist "report.pdf"