Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 131:45900148ca9e

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planemo upload
author kkonganti
date Fri, 05 Jul 2024 09:31:14 -0400
parents 04f6ac8ca13c
children cbb06f201be5
comparison
equal deleted inserted replaced
130:04f6ac8ca13c 131:45900148ca9e
3 <requirements> 3 <requirements>
4 <container type="docker">quay.io/biocontainers/nextflow:24.04.2--hdfd78af_0</container> 4 <container type="docker">quay.io/biocontainers/nextflow:24.04.2--hdfd78af_0</container>
5 </requirements> 5 </requirements>
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 time_stamp=\$(date +%Y-%m-%d-%s);
9 work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
10 input_path=\$(pwd)"/cpipes-input"; 8 input_path=\$(pwd)"/cpipes-input";
11 mkdir -p "\${input_path}" || exit 1; 9 mkdir -p "\${input_path}" || exit 1;
12 #import re 10 #import re
13 #if (str($input_read_type_cond.input_read_type) == "single_long"): 11 #if (str($input_read_type_cond.input_read_type) == "single_long"):
14 #for _, $unpaired in enumerate($input_read_type_cond.input): 12 #for _, $unpaired in enumerate($input_read_type_cond.input):
69 --centrifuge_extract_bug '${centrifuge_extract_bug}' 67 --centrifuge_extract_bug '${centrifuge_extract_bug}'
70 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 68 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
71 --seqkit_rmdup_run true 69 --seqkit_rmdup_run true
72 #end if 70 #end if
73 -profile gxkubernetes; 71 -profile gxkubernetes;
74 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1; 72 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" "./multiqc_report.html" || exit 1;
75 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs || exit 1; 73 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" "kraken2_extract_contigs" || exit 1;
76 ]]></command> 74 ]]></command>
77 <inputs> 75 <inputs>
78 <conditional name="input_read_type_cond"> 76 <conditional name="input_read_type_cond">
79 <param name="input_read_type" type="select" label="Select the read collection type"> 77 <param name="input_read_type" type="select" label="Select the read collection type">
80 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 78 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>