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biopet.biopet
Commits
091cde73
Commit
091cde73
authored
Mar 01, 2017
by
akaljuvee
Browse files
the same but with scala's multi-line string
parent
12da2fa8
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
View file @
091cde73
...
...
@@ -47,17 +47,19 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
}
def
cmdLine
=
required
(
executable
)
+
"-t"
+
required
(
analysistype
)
+
"-o"
+
required
(
outputvcf
)
+
required
(
"-t"
,
analysistype
)
+
required
(
"-o"
,
outputvcf
)
+
required
(
input
)
+
createEmptyOutputIfNeeded
// when no variants are found then the tool doesn't generate the output file either, in Biopet it's needed that the empty file would be there
def
createEmptyOutputIfNeeded
=
Array
(
"c=$?"
,
"if [ $c -eq 0 ] && [ ! -f "
+
outputvcf
+
" ]; then"
,
"echo '##fileformat=VCFv4.2' > "
+
outputvcf
,
"echo '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO' >> "
+
outputvcf
,
"fi"
,
"exit $c"
).
mkString
(
"\n"
,
"\n"
,
"\n"
)
private
def
createEmptyOutputIfNeeded
=
s
"""
|c=$$?
|if [ $$c -eq 0 ] && [ ! -f $outputvcf ]; then
| echo '##fileformat=VCFv4.2' > $outputvcf
| echo '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO' >> $outputvcf
|fi
|exit $$c"""
.
stripMargin
}
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