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Unverified Commit f02b671c authored by Ruben Vorderman's avatar Ruben Vorderman Committed by GitHub
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Merge pull request #33 from biowdl/fix_validateFastq 

fix missing space after toolcommand
parents a8523586 788e0553
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with 4 additions and 4 deletions
biopet.wdl
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...@@ -324,8 +324,8 @@ task ValidateAnnotation { ...@@ -324,8 +324,8 @@ task ValidateAnnotation {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
${toolCommand} \ ${toolCommand} \
${"-r" + refRefflat} \ ${"-r " + refRefflat} \
${"-g" + gtfFile} \ ${"-g " + gtfFile} \
-R ${refFasta} -R ${refFasta}
} }
...@@ -355,7 +355,7 @@ task ValidateFastq { ...@@ -355,7 +355,7 @@ task ValidateFastq {
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
${toolCommand}\ ${toolCommand} \
--fastq1 ${fastq1} \ --fastq1 ${fastq1} \
${"--fastq2 " + fastq2} ${"--fastq2 " + fastq2}
} }
...@@ -386,7 +386,7 @@ task ValidateVcf { ...@@ -386,7 +386,7 @@ task ValidateVcf {
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
${toolCommand}\ ${toolCommand} \
-i ${vcfFile} \ -i ${vcfFile} \
-R ${refFasta} -R ${refFasta}
} }
......
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