Commit 401eda6f authored by Lena Hersemann's avatar Lena Hersemann

set '--outReadsUnmapped Fastx' to always report non-mapping reads in separate fastq files

parent 8d2d605f
......@@ -58,7 +58,7 @@ val pePairingEnabled = !doArgs["disable-pe-pairing"]!!.toBoolean()
//val extraStarParams = doArgs["star-params"] ?:
// "--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3"
val extraStarParams = System.getenv("STAR_PARAMS").takeIf { it!=null } ?:
"--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3"
"--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSJfilterCountUniqueMin 8 3 3 3"
......
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