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Commit 830a39b8 authored by Peter van 't Hof's avatar Peter van 't Hof
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Revert "Fixing output" 

This reverts commit 17af04e8
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...@@ -16,7 +16,7 @@ task fastqc { ...@@ -16,7 +16,7 @@ task fastqc {
Int? kmers Int? kmers
String? dir String? dir
# Chops of the .gz extension if present. # Chops of the .gz extension if present.
String name = sub(sub(sub(seqFile, "\\.gz$",""), "\\.fq$",""), "\\.fastq$","") String name = sub(sub(seqFile, "\\.gz$",""), "\\.fq$|\\.fastq$","")
# This regex chops of the extension and replaces it with _fastqc for the reportdir. # This regex chops of the extension and replaces it with _fastqc for the reportdir.
# Just as fastqc does it. # Just as fastqc does it.
String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc") String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
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