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allow HGFA to be set in local config #32

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allow HGFA to be set in local config #32

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11 changes: 8 additions & 3 deletions src/main/groovy/Ximmer.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -173,10 +173,10 @@ class Ximmer {
throw new IllegalStateException("The analysis pipeline configuration file could not be found at the expected location: $pipelineConfigFile\n\nHave you run the installer?")

ConfigObject pipelineCfg = new ConfigSlurper().parse(pipelineConfigFile.text)
if(!pipelineCfg.containsKey('HGFA'))
if(!pipelineCfg.containsKey('HGFA') && !cfg.containsKey('HGFA'))
throw new IllegalArgumentException("Please set the HGFA parameter to your human genome reference in the config file at: $pipelineConfigFile")

File hgfa = new File(pipelineCfg.HGFA)
File hgfa = new File(pipelineCfg.HGFA || cfg.HGFA)
if(!hgfa.exists())
throw new IllegalArgumentException("The configured reference file $hgfa does not exist. Please check the HGFA entry in $pipelineConfigFile")

Expand Down Expand Up @@ -360,6 +360,7 @@ class Ximmer {
List excludeRegionsParam = []
List excludeGenesParam = []
List geneFilterParam = []
List genomeReferenceParam = []

synchronized(analysisLock) { // Avoid any potential multi-threading issues since all the below
// are reading from non-threadsafe maps, config objects, etc.
Expand Down Expand Up @@ -407,6 +408,10 @@ class Ximmer {
if(cfg.containsKey('exclude_genes')) {
excludeGenesParam = ["-p", "exclude_genes=" + cfg.exclude_genes]
}

if(cfg.containsKey('HGFA')) {
genomeFastaParam = ["-p", "HGFA=" + cfg.HGFA]
}
}


Expand Down Expand Up @@ -437,7 +442,7 @@ class Ximmer {
"-p", "target_bed=$targetRegionsPath",
"-p", /sample_id_mask="$sampleIdMask"/,
"-p", "imgpath=${runDir.name}/#batch#/report/",
] + this.geneListParameters + minCatOpt + excludeRegionsParam + geneFilterParam + excludeGenesParam + drawCnvsParam + [
] + this.geneListParameters + minCatOpt + excludeRegionsParam + geneFilterParam + excludeGenesParam + drawCnvsParam + genomeFastaParam + [
"$ximmerBase/eval/pipeline/exome_cnv_pipeline.groovy"
] + bamFiles + vcfFiles + (enableTruePositives ? ["true_cnvs.bed"] : [])

Expand Down