Commit 8b2eaaaf authored by Holger Brandl's avatar Holger Brandl

save cached jar next to script until #5 is fixed.

parent dc74d040
......@@ -84,10 +84,11 @@ for (fastqFile in fastqFiles) {
// --quantMode GeneCounts see https://groups.google.com/forum/#!searchin/rna-star/GeneCounts/rna-star/gZRJx3ElRNo/p5FjBYKuY00J
// --outSJfilterCountUniqueMin see https://groups.google.com/forum/#!topic/rna-star/_1BeAlGUmpA
val fastqBaseName = fastqFile.name.replace(".fastq.gz", "")
val fastqBaseName = fastqFile.name.removeSuffix(".gz").removeSuffix(".fastq")
val optionalZcat = if (fastqFile.name.endsWith("gz")) "--readFilesCommand zcat" else ""
val cmd = """
STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --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 --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
mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
samtools index ${fastqBaseName}.bam
""".trimIndent()
......
......@@ -10,6 +10,6 @@ source $NGS_TOOLS/dge_workflow/dge_utils.sh
#git clone https://github.com/holgerbrandl/kutils && cd kutils && gradle install && cd .. && rm -rf kutils
star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 test.fastq
star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 ~/test.fastq
mailme "test"
\ No newline at end of file
mailme "star test done"
\ No newline at end of file
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