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Commit 8ed04648 authored by Ruben Vorderman's avatar Ruben Vorderman
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add allow contain

parent 871a562e
Branches BIOWDL-279
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bowtie.wdl
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...@@ -33,6 +33,7 @@ task Bowtie { ...@@ -33,6 +33,7 @@ task Bowtie {
Int? k Int? k
Boolean best = false Boolean best = false
Boolean strata = false Boolean strata = false
Boolean allowContain = false
String? samRG String? samRG
Int threads = 1 Int threads = 1
Int memory = 8 Int memory = 8
...@@ -55,6 +56,7 @@ task Bowtie { ...@@ -55,6 +56,7 @@ task Bowtie {
~{"-k " + k} \ ~{"-k " + k} \
~{true="--best" false="" best} \ ~{true="--best" false="" best} \
~{true="--strata" false="" strata} \ ~{true="--strata" false="" strata} \
~{true="--allow-contain" false="" allowContain} \
~{"--threads " + threads} \ ~{"--threads " + threads} \
~{"--sam-RG '" + samRG}~{true="'" false="" defined(samRG)} \ ~{"--sam-RG '" + samRG}~{true="'" false="" defined(samRG)} \
~{sub(indexFiles[0], "(\.rev)?\.[0-9]\.ebwt$", "")} \ ~{sub(indexFiles[0], "(\.rev)?\.[0-9]\.ebwt$", "")} \
......
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