Change argument name

src/star/star_align_reads/config.vsh.yaml

@@ -73,11 +73,11 @@ argument_groups:
         direction: output
         example: splice_junctions.tsv
       - type: file
-        name: --transcriptome
+        name: --reads_aligned_to_transcriptome
         required: false
-        description: The output file containing the alignments to transcriptome in BAM formats.
+        description: The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM.
         direction: output
-        example: transcriptome.bam
+        example: transcriptome_aligned.bam
 # other arguments are defined in a separate file
 __merge__: argument_groups.yaml
 resources:

src/star/star_align_reads/script.py

@@ -59,7 +59,7 @@
     "splice_junctions": "SJ.out.tab",
     "unmapped": "Unmapped.out.mate1",
     "unmapped_r2": "Unmapped.out.mate2", 
-    "transcriptome": "Aligned.toTranscriptome.out.bam"
+    "reads_aligned_to_transcriptome": "Aligned.toTranscriptome.out.bam"
 }
 output_paths = {name: par[name] for name in expected_outputs.keys()}
 for name in expected_outputs.keys():

src/star/star_align_reads/test.sh

@@ -98,7 +98,7 @@ echo "> Run star_align_reads on SE"
   --reads_per_gene "reads_per_gene.tsv" \
   --outSJtype Standard \
   --splice_junctions "splice_junctions.tsv" \
-  --transcriptome "transcriptome.bam" \
+  --reads_aligned_to_transcriptome "transcriptome_aligned.bam" \
   ${meta_cpus:+---cpus $meta_cpus}
 
 # TODO: Test data doesn't contain any chimeric reads yet
@@ -112,7 +112,7 @@ assert_file_exists "reads_per_gene.tsv"
 # assert_file_exists "chimeric_junctions.tsv"
 assert_file_exists "splice_junctions.tsv"
 assert_file_exists "unmapped.sam"
-assert_file_exists "transcriptome.bam"
+assert_file_exists "transcriptome_aligned.bam"
 
 echo ">> Check if output contents are not empty"
 assert_file_not_empty "output.sam"
@@ -121,7 +121,7 @@ assert_file_not_empty "reads_per_gene.tsv"
 # assert_file_not_empty "chimeric_junctions.tsv"
 # assert_file_not_empty "splice_junctions.tsv" # TODO: test data doesn't contain any splice junctions yet
 assert_file_not_empty "unmapped.sam"
-assert_file_not_empty "transcriptome.bam"
+assert_file_not_empty "transcriptome_aligned.bam"
 
 echo ">> Check if output contents are correct"
 assert_file_contains "log.txt" "Number of input reads \\|	2"