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tasks/trimmomatic.wdl
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| @@ -3,12 +3,11 @@ task trimmomatic { | |||
| File read2 | |||
| File adapter | |||
| String baseout | |||
| String baseout_gz = baseout + ".fq.gz" | |||
| String docker | |||
| String cluster | |||
| 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 { | |||
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