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

dge_workflow/star_align.kts

@@ -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()

dge_workflow/testdata/featcounts_deseq/test_star.sh

@@ -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