[med-svn] [Git][med-team/mecat2][master] Write autopkgtest

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / mecat2


Commits:
a72a0409 by Shayan Doust at 2020-07-03T14:55:21+01:00
Write autopkgtest

- - - - -


1 changed file:

- debian/tests/run-unit-test


Changes:

=====================================
debian/tests/run-unit-test
=====================================
@@ -23,3 +23,20 @@ mecat trim ecoli_config_file.txt
 
 # Assemble contigs using the trimmed reads
 mecat assemble ecoli_config_file.txt
+
+# Now, at least check that we have the resulted files and they have something in them
+CORRECTED_READS="ecoli/1-consensus/cns_reads_list.txt"
+CORRECTED_READS_TRIMMING="ecoli/1-consensus/cns_final.fasta"
+TRIMMED_READS="ecoli/2-trim_bases/trimReads.fasta"
+ASSEMBLED_CONTIGS="ecoli/4-fsa/contigs.fasta"
+
+for FILE in $CORRECTED_READS $CORRECTED_READS_TRIMMING $TRIMMED_READS $ASSEMBLED_CONTIGS
+do
+	if [ ! -s "$FILE" ]
+	then
+		echo "[FAIL] $FILE should have data in it, but doesn't or the file doesn't exist."
+		exit 1
+	else
+		echo "[PASS] $FILE exists and has data in it."
+	fi
+done



View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/a72a0409243b5d21479262fd14728f55c3342480

-- 
View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/a72a0409243b5d21479262fd14728f55c3342480
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