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lines changed Original file line number Diff line number Diff line change @@ -349,7 +349,7 @@ process alignment {
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}
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MQ = " "
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'''
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- STAR --outSAMattrRGline !{rgline} --outSAMmapqUnique !{params.STAR_MapqUnique } --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMstrandField intronMotif --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimOutJunctionFormat 1 --twopassMode Basic --outReadsUnmapped None --runThreadN !{align_threads} --genomeDir . --sjdbGTFfile !{gtf} --readFilesCommand zcat --readFilesIn !{input_f1} !{input_f2} --outStd SAM | samblaster --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag}.bam /dev/stdin
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+ STAR --outSAMattrRGline !{rgline} --outSAMmapqUnique !{params.STAR_mapqUnique } --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMstrandField intronMotif --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimOutJunctionFormat 1 --twopassMode Basic --outReadsUnmapped None --runThreadN !{align_threads} --genomeDir . --sjdbGTFfile !{gtf} --readFilesCommand zcat --readFilesIn !{input_f1} !{input_f2} --outStd SAM | samblaster --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag}.bam /dev/stdin
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mv Chimeric.out.junction STAR.!{file_tag}.Chimeric.SJ.out.junction
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mv SJ.out.tab STAR.!{file_tag}.SJ.out.tab
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mv Log.final.out STAR.!{file_tag}.Log.final.out
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