Commit 9e373320 authored by khalid's avatar khalid
Browse files

set DESeq2 script

parent 92e3f55c
......@@ -15,4 +15,4 @@ rule <step_name>__deseq2:
tx2gene = config["<step_name>__deseq2_tx2gene"],
annotations = config["<step_name>__deseq2_annotations"],
script:
config["<step_name>__deseq2_command"]
\ No newline at end of file
config["<step_name>__deseq2_script"]
\ No newline at end of file
......@@ -18,4 +18,4 @@ rule <step_name>__edger:
dispersion = config["<step_name>__edger_dispersion"],
testType = config["<step_name>__edger_testType"],
script:
config["<step_name>__edger_command"]
\ No newline at end of file
config["<step_name>__edger_script"]
\ No newline at end of file
......@@ -53,7 +53,7 @@ elif config["SeOrPe"] == "SE":
"-x {params.indexPrefix} "
"--rg-id ID:WAW --rg SM:{wildcards.sample} "
#"-S "#output in sam format
" -Ub{input.read} 2> {log} "
"-U {input.read} 2> {log} "
"| samtools view -b 2>> {log} "
"| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
"samtools index -@ {threads} {output.bam} 2>> {log}"
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