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fix input patterns with dir in the pattern causing error / exception

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ssadedin committed Aug 12, 2019
1 parent ddc175c commit 2b591672dfc9d21db3a98fbd9b713a299be77377
@@ -123,8 +123,8 @@ class InputSplitter {
List<PipelineFile> sortNumericThenLexically(Pattern regex, List<Integer> skipGroups, List<PipelineFile> v) {
return v.sort { PipelineFile f1, PipelineFile f2 ->

String i1 = f1.name
String i2 = f2.name
String i1 = f1.path
String i2 = f2.path

// Match
Matcher m1 = regex.matcher(i1)
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@@ -0,0 +1,6 @@
source ../testsupport.sh

run cases/*.gz controls/*.gz

grep -q 'The inputs are cases/BP1-10_R1.fastq.gz cases/BP1-10_R2.fastq.gz$' test.out || err "Failed to see correct inputs printed"

@@ -0,0 +1,14 @@
/*
fastqCaseFormat=cases/%_R*.fastq.gz and the files from that run are cases/EKL14-10_R1.fastq.gz, cases/EKL14-10_R2.fastq.gz, controls/SRX372044_R1.fastq.gz, controls/SRX372044_R2.fastq.gz
*/

fastq_dedupe = {
println "The inputs are $inputs"
}

fastqCaseFormat="cases/%_R*.fastq.gz"
fastqControlFormat="controls/%_R*.fastq.gz"

run {
fastqCaseFormat * [ fastq_dedupe ]
}

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