Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 86:7e421f421b5e

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 17:18:04 -0400
parents 022230c283f2
children 34d411a7bd4f
comparison
equal deleted inserted replaced
85:022230c283f2 86:7e421f421b5e
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input || exit 1; 9 mkdir -p cpipes-input || exit 1;
10 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
11 #import re
11 #if (str($input_read_type_cond.input_read_type) == "single_long"): 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
12 #for _, $unpaired in enumerate($input_read_type_cond.input): 13 #for _, $unpaired in enumerate($input_read_type_cond.input):
13 #set read1 = str($unpaired.name) 14 #set read1 = str($unpaired.name)
14 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): 15 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
15 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) 16 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext)
16 #end if 17 #end if
17 ln -sf '$unpaired' './cpipes-input/$read1'; 18 ln -sf '$unpaired' './cpipes-input/$read1';
18 #end for 19 #end for
19 #elif (str($input_read_type_cond.input_read_type) == "paired"): 20 #elif (str($input_read_type_cond.input_read_type) == "paired"):
20 #for _, $pair in enumerate($input_read_type_cond.input_pair) 21 #for _, $pair in enumerate($input_read_type_cond.input_pair)
21 #set read_R1 = str($pair.forward.name) 22 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
22 #set read_R2 = str($pair.reverse.name) 23 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
23 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): 24 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
24 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) 25 #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext)
25 #end if 26 #end if
26 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): 27 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
27 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) 28 #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext)
28 #end if 29 #end if
29 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 30 ln -sf '$pair.forward' './cpipes-input/$read_R1';
30 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 31 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
31 #end for 32 #end for
32 #end if 33 #end if