fixed more xargs

lskatz · Nov 16, 2016 · b90eae9 · b90eae9
1 parent 3b16d89
commit b90eae9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/scripts/launch_set.pl b/scripts/launch_set.pl
@@ -611,7 +611,7 @@ sub variantCalls{
     }
     if(!-e $regionsFile){
       system("rm -fv $regionsFile.*.tmp");
-      my $command="samtools view -H $initBam | grep \"\@SQ\" | sed 's/^.*SN://g' | cut -f 1 | xargs -I {} -n 1 -P $$settings{numcpus} sh -c \"samtools mpileup -suf $ref -r '{}' $initBam | bcftools call -c | grep -v '^#' | cut -f 1,2 > $regionsFile.'{}'.tmp \" ";
+      my $command="samtools view -H $initBam | grep \"\@SQ\" | sed 's/^.*SN://g' | cut -f 1 | xargs -n 1 -P $$settings{numcpus} sh -c \"samtools mpileup -suf $ref -r '$0' $initBam | bcftools call -c | grep -v '^#' | cut -f 1,2 > $regionsFile.'$0'.tmp \" ";
       $sge->pleaseExecute($command,{numcpus=>$$settings{numcpus},jobname=>"snpPositionDiscovery"});
       $sge->wrapItUp();
 

diff --git a/scripts/mergeVcf.sh b/scripts/mergeVcf.sh
@@ -67,7 +67,7 @@ echo "$script: temporary directory is $TEMPDIR";
 echo "$script: Running bcftools merge";
 export IN;
 export script;
-echo "$REGION" | xargs -P $NUMCPUS -n 1 -I {} bash -c 'echo "$script: merging SNPs in {}"; out='$TEMPDIR'/merged.$$.vcf; bcftools merge --merge all --regions "{}" --force-samples -o $out $IN && bgzip $out && tabix $out.gz && echo "$script: finished with region {}";'
+echo "$REGION" | xargs -P $NUMCPUS -n 1 bash -c 'echo "$script: merging SNPs in $0"; out='$TEMPDIR'/merged.$$.vcf; bcftools merge --merge all --regions "$0" --force-samples -o $out $IN && bgzip $out && tabix $out.gz && echo "$script: finished with region $0";'
 if [ $? -gt 0 ]; then
   echo "$script: ERROR with bcftools merge"
   rm -rvf $TEMPDIR;