Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 116:b6fcae1983cb

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 10:45:24 -0400
parents 345d0a16f026
children b9c76c256e2c
comparison
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115:a56f9d099aa5 116:b6fcae1983cb
6 <version_command>nextflow -version</version_command> 6 <version_command>nextflow -version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p cpipes-input || exit 1; 8 mkdir -p cpipes-input || exit 1;
9 pwd_path=\$(pwd); 9 pwd_path=\$(pwd);
10 time_stamp=\$(date +%Y-%m-%d-%s); 10 time_stamp=\$(date +%Y-%m-%d-%s);
11 work_dir="\${pwd_path}/centriflaken_work_dir-"\${time_stamp}; 11 work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
12 mkdir -p \$work_dir || exit 1; 12 mkdir -p \$work_dir || exit 1;
13 #import re 13 #import re
14 #if (str($input_read_type_cond.input_read_type) == "single_long"): 14 #if (str($input_read_type_cond.input_read_type) == "single_long"):
15 #for _, $unpaired in enumerate($input_read_type_cond.input): 15 #for _, $unpaired in enumerate($input_read_type_cond.input):
16 #set read1 = str($unpaired.name) 16 #set read1 = str($unpaired.name)
36 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 36 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
37 #end for 37 #end for
38 #end if 38 #end if
39 $__tool_directory__/0.4.2/cpipes 39 $__tool_directory__/0.4.2/cpipes
40 --pipeline $input_read_type_cond.pipeline_cond.pipeline 40 --pipeline $input_read_type_cond.pipeline_cond.pipeline
41 -work-dir \${work_dir}
41 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 42 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
42 --fq_single_end true 43 --fq_single_end true
43 --flye_genome_size '${genome_size}' 44 --flye_genome_size '${genome_size}'
44 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 45 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
45 --flye_nano_corr true --flye_nano_raw false 46 --flye_nano_corr true --flye_nano_raw false