Commit eff9c5cd authored by bow's avatar bow
Browse files

Fix wrong threads setting in Bowtie and Bwa wrappers

parent 544eb3a0
...@@ -61,7 +61,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -61,7 +61,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
/** return commandline to execute */ /** return commandline to execute */
def cmdLine = { def cmdLine = {
required(executable) + required(executable) +
optional("--threads", nCoresRequest) + optional("--threads", threads) +
conditional(sam, "--sam") + conditional(sam, "--sam") +
conditional(best, "--best") + conditional(best, "--best") +
conditional(strata, "--strata") + conditional(strata, "--strata") +
......
...@@ -51,6 +51,7 @@ class BwaAln(val root: Configurable) extends Bwa { ...@@ -51,6 +51,7 @@ class BwaAln(val root: Configurable) extends Bwa {
/** Returns command to execute */ /** Returns command to execute */
def cmdLine = required(executable) + def cmdLine = required(executable) +
required("aln") + required("aln") +
optional("-t", threads) +
optional("-n", n) + optional("-n", n) +
optional("-o", o) + optional("-o", o) +
optional("-e", e) + optional("-e", e) +
......
...@@ -77,7 +77,7 @@ class BwaMem(val root: Configurable) extends Bwa { ...@@ -77,7 +77,7 @@ class BwaMem(val root: Configurable) extends Bwa {
required("mem") + required("mem") +
optional("-k", k) + optional("-k", k) +
optional("-r", r) + optional("-r", r) +
optional("-t", nCoresRequest) + optional("-t", threads) +
optional("-R", R) + optional("-R", R) +
conditional(M, "-M") + conditional(M, "-M") +
conditional(S, "-S") + conditional(S, "-S") +
......
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