adjust argument names, reduce test data size

src/rseqc/rseqc_bamstat/config.vsh.yaml

@@ -17,11 +17,13 @@ authors:
 argument_groups:
 - name: "Input"
   arguments: 
-  - name: "--input"
+  - name: "--input_file"
+    alternatives: -i
     type: file 
     required: true
     description: Input alignment file in BAM or SAM format.
-  - name: "--map_qual"
+  - name: "--mapq"
+    alternatives: -q
     type: integer
     example: 30 
     description: |
@@ -45,10 +47,8 @@ test_resources:
 
 engines:
 - type: docker
-  image: ubuntu:22.04
-  setup:   
-    - type: apt
-      packages: [ python3-pip ]
+  image: python:3.10
+  setup:
     - type: python
       packages: [ RSeQC ]
     - type: docker

src/rseqc/rseqc_bamstat/script.sh

@@ -4,6 +4,6 @@
 set -eo pipefail 
 
 bam_stat.py \
-    --input "${par_input}" \
-    ${par_map_qual:+--mapq "${par_map_qual}"} \
+    --input-file "${par_input_file}" \
+    ${par_mapq:+--mapq "${par_mapq}"} \
 > $par_output

src/rseqc/rseqc_bamstat/test.sh

@@ -2,14 +2,14 @@
 
 # define input and output for script
 
-input_bam="test.paired_end.sorted.bam"
+input_bam="sample.bam"
 output_summary="mapping_quality.txt"
 
 # run executable and tests
 echo "> Running $meta_functionality_name."
 
 "$meta_executable" \
-    --input "$meta_resources_dir/test_data/$input_bam" \
+    --input_file "$meta_resources_dir/test_data/$input_bam" \
     --output "$output_summary"
 
 exit_code=$?
@@ -26,15 +26,15 @@ diff "$meta_resources_dir/test_data/ref_output.txt" "$meta_resources_dir/$output
 
 echo ">>> Test 2: Test with non-default mapping quality threshold"
 
-output_summary="mapping_quality_mapq_30.txt"
+output_summary="mapping_quality_mapq_50.txt"
 
 # run executable and tests
 echo "> Running $meta_functionality_name."
 
 "$meta_executable" \
-    --input "$meta_resources_dir/test_data/$input_bam" \
+    --input_file "$meta_resources_dir/test_data/$input_bam" \
     --output "$output_summary" \
-    --map_qual 50
+    --mapq 50
 
 exit_code=$?
 [[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1

src/rseqc/rseqc_bamstat/test_data/ref_output.txt

@@ -3,20 +3,20 @@
 #All numbers are READ count
 #==================================================
 
-Total records:                          200
+Total records:                          90
 
 QC failed:                              0
 Optical/PCR duplicate:                  0
 Non primary hits                        0
-Unmapped reads:                         3
-mapq < mapq_cut (non-unique):           1
+Unmapped reads:                         1
+mapq < mapq_cut (non-unique):           0
 
-mapq >= mapq_cut (unique):              196
-Read-1:                                 99
-Read-2:                                 97
-Reads map to '+':                       98
-Reads map to '-':                       98
-Non-splice reads:                       196
+mapq >= mapq_cut (unique):              89
+Read-1:                                 45
+Read-2:                                 44
+Reads map to '+':                       44
+Reads map to '-':                       45
+Non-splice reads:                       89
 Splice reads:                           0
-Reads mapped in proper pairs:           192
+Reads mapped in proper pairs:           88
 Proper-paired reads map to different chrom:0

src/rseqc/rseqc_bamstat/test_data/ref_output_mapq.txt

@@ -3,20 +3,20 @@
 #All numbers are READ count
 #==================================================
 
-Total records:                          200
+Total records:                          90
 
 QC failed:                              0
 Optical/PCR duplicate:                  0
 Non primary hits                        0
-Unmapped reads:                         3
-mapq < mapq_cut (non-unique):           20
+Unmapped reads:                         1
+mapq < mapq_cut (non-unique):           6
 
-mapq >= mapq_cut (unique):              177
-Read-1:                                 88
-Read-2:                                 89
-Reads map to '+':                       96
-Reads map to '-':                       81
-Non-splice reads:                       177
+mapq >= mapq_cut (unique):              83
+Read-1:                                 42
+Read-2:                                 41
+Reads map to '+':                       44
+Reads map to '-':                       39
+Non-splice reads:                       83
 Splice reads:                           0
-Reads mapped in proper pairs:           175
+Reads mapped in proper pairs:           83
 Proper-paired reads map to different chrom:0