Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 88:0c59342d0144

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"planemo upload"
author kkonganti
date Thu, 14 Jul 2022 09:38:11 -0400
parents 34d411a7bd4f
children 55a686167e40
comparison
equal deleted inserted replaced
87:34d411a7bd4f 88:0c59342d0144
17 #end if 17 #end if
18 ln -sf '$unpaired' './cpipes-input/$read1'; 18 ln -sf '$unpaired' './cpipes-input/$read1';
19 #end for 19 #end for
20 #elif (str($input_read_type_cond.input_read_type) == "paired"): 20 #elif (str($input_read_type_cond.input_read_type) == "paired"):
21 #for _, $pair in enumerate($input_read_type_cond.input_pair) 21 #for _, $pair in enumerate($input_read_type_cond.input_pair)
22 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) 22 #set read_R1 = re.sub('[^\s\w\-]', '_', str($pair.forward.name))
23 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) 23 #set read_R2 = re.sub('[^\s\w\-]', '_', str($pair.reverse.name))
24 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): 24 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
25 #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext) 25 #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext)
26 #end if 26 #end if
27 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): 27 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
28 #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext) 28 #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext)