Commit 3ec24143 authored by Holger Brandl's avatar Holger Brandl

added workaround for network filesystem problems

parent eaf2dec9
...@@ -130,6 +130,7 @@ for (fastqFile in fastqFiles) { ...@@ -130,6 +130,7 @@ for (fastqFile in fastqFiles) {
val cmd = """ val cmd = """
STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3 STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
sleep 5 # to avoid filsystem issues on network volumnes
mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
samtools index ${fastqBaseName}.bam samtools index ${fastqBaseName}.bam
""".trimIndent() """.trimIndent()
......
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