remove test data

src/star/star_align/config.vsh.yaml

@@ -80,7 +80,6 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
-  - path: test_data
 engines:
   - type: docker
     image: python:3.12-slim

src/star/star_align/test.sh

@@ -7,7 +7,8 @@ meta_executable="target/docker/star/star_align/star_align"
 meta_resources_dir="src/star/star_align"
 ## VIASH END
 
-#############################################
+#########################################################################################
+
 # helper functions
 assert_file_exists() {
   [ -f "$1" ] || (echo "File '$1' does not exist" && exit 1)
@@ -34,7 +35,7 @@ assert_file_not_contains_regex() {
   grep -q -E "$2" "$1" && (echo "File '$1' contains '$2' but shouldn't" && exit 1)
 }
 
-#############################################
+#########################################################################################
 echo "> Prepare test data"
 
 cat > reads_R1.fastq <<'EOF'
@@ -81,6 +82,7 @@ STAR \
   --genomeSAindexNbases 2
 
 #########################################################################################
+
 mkdir star_align_se
 cd star_align_se
 
@@ -92,11 +94,11 @@ echo "> Run star_align on SE"
   --log "log.txt" \
   --outReadsUnmapped "Fastx" \
   --unmapped "unmapped.sam" \
-  ${meta_cpus:+---cpus $meta_cpus} \
   --quantMode "TranscriptomeSAM;GeneCounts" \
   --reads_per_gene "reads_per_gene.tsv" \
   --outSJtype Standard \
-  --splice_junctions "splice_junctions.tsv"
+  --splice_junctions "splice_junctions.tsv" \
+  ${meta_cpus:+---cpus $meta_cpus}
 
 # TODO: Test data doesn't contain any chimeric reads yet
 # --chimOutType "Junctions" \
@@ -130,40 +132,42 @@ assert_file_contains "unmapped.sam" "ACCCGCAAGATTAGGCTCCGTACAC"
 
 cd ..
 
-# #########################################################################################
-# mkdir star_align_pe_minimal
-# cd star_align_pe_minimal
-
-# echo ">> Run star_align on PE"
-# "$meta_executable" \
-#   --input "$meta_resources_dir/test_data/a_R1.1.fastq" \
-#   --input "$meta_resources_dir/test_data/a_R1.2.fastq" \
-#   --input_r2 "$meta_resources_dir/test_data/a_R2.1.fastq" \
-#   --input_r2 "$meta_resources_dir/test_data/a_R2.2.fastq" \
-#   --genomeDir "../index/" \
-#   --aligned_reads "output.sam" \
-#   --log "log.txt" \
-#   --outReadsUnmapped "Fastx" \
-#   --unmapped "unmapped.bam" \
-#   --unmapped_r2 "unmapped_r2.bam" \
-#   ${meta_cpus:+---cpus $meta_cpus}
-
-# echo ">> Check if output exists"
-# [ ! -f "output.sam" ] && echo ">> output.sam does not exist" && exit 1
-# [ ! -f "log.txt" ] && echo ">> log.txt does not exist" && exit 1
-# [ ! -f "unmapped.bam" ] && echo ">> unmapped.bam does not exist" && exit 1
-# [ ! -f "unmapped_r2.bam" ] && echo ">> unmapped_r2.bam does not exist" && exit 1
-
-# cd ..
-# #########################################################################################
-
-# # TODO: check whether optional outputs work: 
-# #   - quantMode "TranscriptomeSAM;GeneCounts"
-# #   - reads_per_gene "reads_per_gene.tsv"
-# #   - chimOutType "Junctions"
-# #   - chimeric_junctions "chimeric_junctions.tsv"
-# #   - outSJtype Standard
-# #   - splice_junctions "splice_junctions.tsv"
-# # TODO: check whether output contents are correct
-
-# echo "> Test successful"
+#########################################################################################
+
+mkdir star_align_pe_minimal
+cd star_align_pe_minimal
+
+echo ">> Run star_align on PE"
+"$meta_executable" \
+  --input ../reads_R1.fastq \
+  --input_r2 ../reads_R2.fastq \
+  --genomeDir ../index/ \
+  --aligned_reads output.bam \
+  --log log.txt \
+  --outReadsUnmapped Fastx \
+  --unmapped unmapped_r1.bam \
+  --unmapped_r2 unmapped_r2.bam \
+  ${meta_cpus:+---cpus $meta_cpus}
+
+echo ">> Check if output exists"
+assert_file_exists "output.bam"
+assert_file_exists "log.txt"
+assert_file_exists "unmapped_r1.bam"
+assert_file_exists "unmapped_r2.bam"
+
+echo ">> Check if output contents are not empty"
+assert_file_not_empty "output.bam"
+assert_file_not_empty "log.txt"
+assert_file_not_empty "unmapped_r1.bam"
+assert_file_not_empty "unmapped_r2.bam"
+
+echo ">> Check if output contents are correct"
+assert_file_contains "log.txt" "Number of input reads \\|	2"
+assert_file_contains "log.txt" "Number of reads unmapped: too short \\|	1"
+assert_file_contains "log.txt" "Uniquely mapped reads number \\|	1"
+
+cd ..
+
+#########################################################################################
+
+echo "> Test successful"