Commit 92bdf700 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix default values and conditionals instead of optionals

parent cb684be5
......@@ -33,7 +33,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var bowtieIndex: String = config("bowtie_index")
/* Input options */
var q: Boolean = config("q", default = true)
var q: Boolean = config("q", default = false)
var qseq: Boolean = config("qseq", default = false)
var f: Boolean = config("f", default = false)
var r: Boolean = config("r", default = false)
......@@ -106,7 +106,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var un_conc_bz2: Option[String] = config("un_conc_bz2")
var al_conc_bz2: Option[String] = config("al_conc_bz2")
var quiet: Boolean = config("quiet", default = true)
var quiet: Boolean = config("quiet", default = false)
var met_file: Option[String] = config("met_file")
var met_stderr: Boolean = config("met_stderr", default = false)
var met: Option[Int] = config("met")
......@@ -122,7 +122,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
/* Performance */
var reorder: Boolean = config("reorder", default = false)
var mm: Boolean = config("mm", default = true)
var mm: Boolean = config("mm", default = false)
/* Other */
var qc_filter: Boolean = config("qc_filter", default = false)
......@@ -150,7 +150,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
optional("--n-ceil", n_ceil) +
optional("--dpad", dpad) +
optional("--gbar", gbar) +
optional("--ignore-quals", ignore_quals) +
conditional(ignore_quals, "--ignore-quals") +
conditional(nofw, "--nofw") +
conditional(norc, "--norc") +
conditional(no_1mm_upfront, "--no-1mm-upfront") +
......@@ -206,8 +206,8 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
conditional(omit_sec_seq, "--omit-sec-seq") +
/* Performance */
optional("--threads", threads) +
optional("--reorder", reorder) +
optional("--mm", mm) +
conditional(reorder, "--reorder") +
conditional(mm, "--mm") +
/* Other */
conditional(qc_filter, "--qc-filter") +
optional("--seed", seed) +
......
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