From 4969605e6f7ab7e7fcf153f83d89b2dc86ab4185 Mon Sep 17 00:00:00 2001 From: Tom Smith Date: Wed, 21 Dec 2016 15:28:31 +0000 Subject: [PATCH] updates samtools sort commands --- pipeline_scRNASeq.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/pipeline_scRNASeq.py b/pipeline_scRNASeq.py index a1686fd..a98fb59 100644 --- a/pipeline_scRNASeq.py +++ b/pipeline_scRNASeq.py @@ -230,7 +230,6 @@ def dedupGSE53638(infile, outfiles): for outfile in outfiles: outfile_tmp = outfile.replace("_deduped.trans.bam", "_temp.trans.bam") - outfile_snip = P.snip(outfile, ".bam") method = P.snip(os.path.basename( os.path.dirname(outfile).replace("dedup_", "")), ".dir") @@ -246,7 +245,7 @@ def dedupGSE53638(infile, outfiles): -I %(infile)s -S %(outfile_tmp)s -L %(outfile)s.log --output-stats=%(outfile)s.stats %(options)s; checkpoint; - samtools sort %(outfile_tmp)s %(outfile_snip)s; + samtools sort %(outfile_tmp)s > %(outfile)s; checkpoint; samtools index %(outfile)s; checkpoint; @@ -524,7 +523,6 @@ def dedupGSE65525(infile, outfiles): for outfile in outfiles: outfile_tmp = outfile.replace("_deduped.trans.bam", "_temp.trans.bam") - outfile_snip = P.snip(outfile, ".bam") method = P.snip(os.path.basename( os.path.dirname(outfile).replace("dedup_", "")), ".dir") @@ -542,7 +540,7 @@ def dedupGSE65525(infile, outfiles): --per-contig --method=%(method)s %(stats_cmd)s -I %(infile)s -S %(outfile_tmp)s -L %(outfile)s.log; checkpoint; - samtools sort %(outfile_tmp)s %(outfile_snip)s; + samtools sort %(outfile_tmp)s > %(outfile)s; checkpoint; samtools index %(outfile)s; rm -rf %(outfile_tmp)s'''