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tasks/trimmomatic.wdl
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| File read2 | File read2 | ||||
| File adapter | File adapter | ||||
| String baseout | String baseout | ||||
| String baseout_gz = baseout + ".fq.gz" | |||||
| String docker | String docker | ||||
| String cluster | String cluster | ||||
| command { | command { | ||||
| trimmomatic PE -threads 20 -phred33 ${read1} ${read2} -baseout ${baseout_gz} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36 | |||||
| trimmomatic PE -threads 20 -phred33 ${read1} ${read2} -baseout ${baseout} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36 | |||||
| } | } | ||||
| runtime { | runtime { |
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