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Fixed handling of paired reads
author estrain
date Tue, 24 Sep 2019 11:03:40 -0400
parents e2b708d5c0d3
children
comparison
equal deleted inserted replaced
23:e2b708d5c0d3 24:280e8868b85e
12 #else if $jobtype.select == "fastq_single" 12 #else if $jobtype.select == "fastq_single"
13 #set outname = $jobtype.fastq1.name 13 #set outname = $jobtype.fastq1.name
14 --fastq $jobtype.fastq1 14 --fastq $jobtype.fastq1
15 #else if $jobtype.select == "fastq_fr" 15 #else if $jobtype.select == "fastq_fr"
16 #set outname = $jobtype.fastq1.name 16 #set outname = $jobtype.fastq1.name
17 --fastq $jobtype.fastq1 --fastq $jobtype.fastq2 17 --fastq $jobtype.fastq1,$jobtype.fastq2
18 #else if $jobtype.select == "fastq_pair" 18 #else if $jobtype.select == "fastq_pair"
19 #set outname = $jobtype.coll.name 19 #set outname = $jobtype.coll.name
20 --fastq $jobtype.coll.forward --fastq $jobtype.coll.reverse 20 --fastq $jobtype.coll.forward,$jobtype.coll.reverse
21 #end if 21 #end if
22 22
23 #if $options.select=="advanced" 23 #if $options.select=="advanced"
24 #if $options.cores 24 #if $options.cores
25 --cores $options.cores 25 --cores $options.cores