Andreas Tille pushed to branch master at Debian Med / fastqc
Commits: 54b4710c by tony mancill at 2020-04-06T15:26:04-07:00 Update fastqc autopkgtests to compare summary output (Closes: #950311) - - - - - f68b71eb by tony mancill at 2020-04-06T15:26:54-07:00 interim changelog - - - - - 939c0d47 by tony mancill at 2020-04-06T15:30:51-07:00 update debian/source/include-binaries after renaming test file Gbp-Dch: ignore - - - - - 88efed42 by tony mancill at 2020-04-06T15:56:42-07:00 Exit non-zero after test failure and adjust location of tests_dir Gbp-Dch: ignore - - - - - 8 changed files: - debian/changelog - debian/source/include-binaries - debian/tests.fastqc/toy.bam → debian/tests.fastqc/toy_bam.bam - debian/tests.fastqc/toy.sam → debian/tests.fastqc/toy_sam.sam - + debian/tests/example_fastqc_expected_summary.txt - debian/tests/run-unit-test - + debian/tests/toy_bam_fastqc_expected_summary.txt - + debian/tests/toy_sam_fastqc_expected_summary.txt Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +fastqc (0.11.9+dfsg-3) UNRELEASED; urgency=medium + + * Team upload. + * Update autopkgtests to compare summary output (Closes: #950311) + + -- tony mancill <[email protected]> Mon, 06 Apr 2020 15:26:31 -0700 + fastqc (0.11.9+dfsg-2) unstable; urgency=medium * Fix and enhance autopkgtest ===================================== debian/source/include-binaries ===================================== @@ -1 +1 @@ -debian/tests.fastqc/toy.bam +debian/tests.fastqc/toy_bam.bam ===================================== debian/tests.fastqc/toy.bam → debian/tests.fastqc/toy_bam.bam ===================================== ===================================== debian/tests.fastqc/toy.sam → debian/tests.fastqc/toy_sam.sam ===================================== ===================================== debian/tests/example_fastqc_expected_summary.txt ===================================== @@ -0,0 +1,11 @@ +PASS Basic Statistics example.fastq +WARN Per base sequence quality example.fastq +PASS Per tile sequence quality example.fastq +PASS Per sequence quality scores example.fastq +WARN Per base sequence content example.fastq +WARN Per sequence GC content example.fastq +PASS Per base N content example.fastq +PASS Sequence Length Distribution example.fastq +PASS Sequence Duplication Levels example.fastq +WARN Overrepresented sequences example.fastq +PASS Adapter Content example.fastq ===================================== debian/tests/run-unit-test ===================================== @@ -2,6 +2,8 @@ set -e pkg="fastqc" +tests_dir="$PWD/debian/tests" +test_failures=0 if [ "$AUTOPKGTEST_TMP" = "" ] ; then AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` @@ -14,26 +16,28 @@ cd $AUTOPKGTEST_TMP find . -name "*.gz" -exec gunzip \{\} \; -for sample in example.fastq toy.sam toy.bam ; do - /usr/bin/fastqc "$sample" - if [ "$sample" = "example.fastq" ] ; then - result=example_fastqc - else - result=toy_fastqc - fi - unzip -q "$result".zip - if grep -q FAIL "$result"/summary.txt ; then +for sample in example.fastq toy_sam.sam toy_bam.bam ; do + /usr/bin/fastqc --extract "$sample" + result="${sample%%.*}_fastqc" + expected="${tests_dir}/${result}_expected_summary.txt" + if ! diff -q "${result}/summary.txt" ${expected} 2>/dev/null ; then + (( test_failures += 1 )) cat <<EOT -There were some failures logged in summary of +Summary results did not match contents of ${expected} for fastqc "$sample" Please investigate! EOT - grep FAIL "$result"/summary.txt else - echo "All passing in: fastqc "$sample" " + echo "Summary results match for: fastqc "$sample" " fi rm -rf "$result"* echo "" done -echo "PASS" +if (( test_failures == 0 )); then + echo "PASS" + exit 0 +fi + +echo "FAIL mismatched fastqc summary count: $test_failures" +exit 1 ===================================== debian/tests/toy_bam_fastqc_expected_summary.txt ===================================== @@ -0,0 +1,10 @@ +PASS Basic Statistics toy_bam.bam +PASS Per base sequence quality toy_bam.bam +FAIL Per sequence quality scores toy_bam.bam +FAIL Per base sequence content toy_bam.bam +FAIL Per sequence GC content toy_bam.bam +PASS Per base N content toy_bam.bam +WARN Sequence Length Distribution toy_bam.bam +PASS Sequence Duplication Levels toy_bam.bam +FAIL Overrepresented sequences toy_bam.bam +PASS Adapter Content toy_bam.bam ===================================== debian/tests/toy_sam_fastqc_expected_summary.txt ===================================== @@ -0,0 +1,10 @@ +PASS Basic Statistics toy_sam.sam +PASS Per base sequence quality toy_sam.sam +FAIL Per sequence quality scores toy_sam.sam +FAIL Per base sequence content toy_sam.sam +FAIL Per sequence GC content toy_sam.sam +PASS Per base N content toy_sam.sam +WARN Sequence Length Distribution toy_sam.sam +PASS Sequence Duplication Levels toy_sam.sam +FAIL Overrepresented sequences toy_sam.sam +PASS Adapter Content toy_sam.sam View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/0afa37784bd5ddd23d57ac77c5d61ba098ed189d...88efed4269c0875f8478d7f9aab136467ce4156b -- View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/0afa37784bd5ddd23d57ac77c5d61ba098ed189d...88efed4269c0875f8478d7f9aab136467ce4156b You're receiving this email because of your account on salsa.debian.org.
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