Add test from nf-core

src/samtools/flagstat/test.sh

@@ -19,8 +19,27 @@ diff "$meta_resources_dir/test_data/a.flagstat" "$meta_resources_dir/test_data/a
 
 rm "$meta_resources_dir/test_data/a.flagstat"
 
-################################################################################
+############################################################################################
+
+echo ">>> Testing $meta_functionality_name with singletons in the input"
+
+"$meta_executable" \
+  --bam "$meta_resources_dir/test_data/test.paired_end.sorted.bam" \
+  --bai "$meta_resources_dir/test_data/test.paired_end.sorted.bam.bai" \
+  --output "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" "$meta_resources_dir/test_data/test_ref.paired_end.sorted.flagstat" || \
+    (echo "Output file chr19.flagstat does not match expected output" && exit 1)
+
+rm "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"
+
 
-echo 
 echo "All tests succeeded!"
 exit 0

src/samtools/flagstat/test_data/script.sh

@@ -1,5 +1,14 @@
 #!/bin/bash
 
 # Download test data from snakemake wrapper
+
 wget https://raw.githubusercontent.com/snakemake/snakemake-wrappers/3a4f7004281efc176fd9af732ad88d00c47d432d/bio/samtools/flagstat/test/mapped/a.bam
-samtools index a.bam
+samtools index a.bam
+# samtools flagstat a.bam > a_ref.flagstat
+
+
+# Download test data from nf-core module
+
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai
+# samtools flagstat test.paired_end.sorted.bam > test_ref.paired_end.sorted.flagstat

src/samtools/flagstat/test_data/test_ref.paired_end.sorted.flagstat

@@ -0,0 +1,13 @@
+200 + 0 in total (QC-passed reads + QC-failed reads)
+0 + 0 secondary
+0 + 0 supplementary
+0 + 0 duplicates
+197 + 0 mapped (98.50% : N/A)
+200 + 0 paired in sequencing
+100 + 0 read1
+100 + 0 read2
+192 + 0 properly paired (96.00% : N/A)
+194 + 0 with itself and mate mapped
+3 + 0 singletons (1.50% : N/A)
+0 + 0 with mate mapped to a different chr
+0 + 0 with mate mapped to a different chr (mapQ>=5)