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Update samtools version
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emmarousseau committed Mar 29, 2024
1 parent 8a5d9d7 commit 4f771f9
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Showing 4 changed files with 11 additions and 4 deletions.
4 changes: 2 additions & 2 deletions src/samtools/flagstat/config.vsh.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name: samtools_flagstat
namespace: samtools
description: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.
keywords: [ stats, mapping, counts, bam, sam, cram]
keywords: [ stats, mapping, counts, bam, sam, cram ]
links:
homepage: https://www.htslib.org/
documentation: https://www.htslib.org/doc/samtools-flagstat.html
Expand Down Expand Up @@ -40,7 +40,7 @@ test_resources:
path: test_data
engines:
- type: docker
image: quay.io/biocontainers/samtools:1.3.1--h9071d68_10
image: quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
setup:
- type: docker
run: |
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5 changes: 3 additions & 2 deletions src/samtools/flagstat/test.sh
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Expand Up @@ -16,7 +16,7 @@ echo ">>> Checking whether output is non-empty"

echo ">>> Checking whether output is correct"
diff "$test_dir/a.flagstat" "$test_dir/a_ref.flagstat" || \
(echo "Output file chr19.flagstat does not match expected output" && exit 1)
(echo "Output file a.flagstat does not match expected output" && exit 1)

rm "$test_dir/a.flagstat"

Expand All @@ -37,10 +37,11 @@ echo ">>> Checking whether output is non-empty"

echo ">>> Checking whether output is correct"
diff "$test_dir/test.paired_end.sorted.flagstat" "$test_dir/test_ref.paired_end.sorted.flagstat" || \
(echo "Output file chr19.flagstat does not match expected output" && exit 1)
(echo "Output file test.paired_end.sorted.flagstat does not match expected output" && exit 1)

rm "$test_dir/test.paired_end.sorted.flagstat"



echo "All tests succeeded!"
exit 0
3 changes: 3 additions & 0 deletions src/samtools/flagstat/test_data/a_ref.flagstat
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
6 + 0 in total (QC-passed reads + QC-failed reads)
6 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
6 + 0 mapped (100.00% : N/A)
6 + 0 primary mapped (100.00% : N/A)
6 + 0 paired in sequencing
3 + 0 read1
3 + 0 read2
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
200 + 0 in total (QC-passed reads + QC-failed reads)
200 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
197 + 0 mapped (98.50% : N/A)
197 + 0 primary mapped (98.50% : N/A)
200 + 0 paired in sequencing
100 + 0 read1
100 + 0 read2
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