Fix bug with tmp files when multiple instances are run in the same di…

…rectory
morispi · Oct 13, 2020 · 2840c63 · 2840c63
1 parent 3be459e
commit 2840c63
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/CONSENT-correct b/CONSENT-correct
@@ -192,8 +192,8 @@ do
 	sort -k1,1 -k 10,10nr -T . --parallel="$nproc" $f > $tmpdir/sorted_$(basename $f)
 	rm $f
 done
-$LRSCf/bin/merge $tmpdir/"$alignments" correction "$tmpdir/sorted_"*
-rm "$tmpdir/sorted_"*
+$LRSCf/bin/merge $tmpdir/"$alignments" correction "$tmpdir/sorted_"$exploded*
+rm "$tmpdir/sorted_"$exploded*
 
 echo "["$(date)"] Correcting the long reads"
 $LRSCf/bin/CONSENT-correction -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"

diff --git a/CONSENT-polish b/CONSENT-polish
@@ -193,8 +193,8 @@ do
 	sort -k6,6 -k 10,10nr -T . --parallel="$nproc" $f > $tmpdir/sorted_$(basename $f)
 	rm $f
 done
-$LRSCf/bin/merge $tmpdir/"tmp_$alignments" polishing "$tmpdir/sorted_"*
-rm "$tmpdir/sorted_"*
+$LRSCf/bin/merge $tmpdir/"tmp_$alignments" polishing "$tmpdir/sorted_"$exploded*
+rm "$tmpdir/sorted_"$exploded*
 $LRSCf/bin/reformatPAF.py $tmpdir/"tmp_$alignments" > $tmpdir/"$alignments"
 rm "$tmpdir/tmp_$alignments"