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annotate hydra.xml @ 0:71976cfc9022 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
author nml
date Mon, 04 Dec 2017 10:25:26 -0500
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children 1abf6b32ecfd
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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1 <tool id="hydra" name="Hydra pipeline" version="0.1.0">
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2 <description>Identifies drug resistance within an NGS dataset</description>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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3 <requirements>
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4 <requirement type="package" version="0.2.2">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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8 quasitools hydra '$forward'
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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10 #if $reverse:
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11 '$reverse'
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12 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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14 #if $mutation_db:
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15 -m '$mutation_db'
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16 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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18 #if $reporting_threshold:
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19 -rt '$reporting_threshold'
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20 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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22 #if $consensus_pct:
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23 -cp '$consensus_pct'
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24 #end if
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26 #if $length_cutoff:
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27 -lc '$length_cutoff'
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28 #end if
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30 #if $score_cutoff:
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31 -sc '$score_cutoff'
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32 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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34 #if $error_rate:
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35 -e '$error_rate'
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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36 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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38 #if $min_qual:
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39 -mq '$min_qual'
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40 #end if
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42 #if $min_depth:
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43 -md '$min_depth'
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44 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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46 #if $min_ac:
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47 -ma '$min_ac'
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48 #end if
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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50 #if $min_freq:
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51 -mf '$min_freq'
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52 #end if
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53
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54 #if $generate_consensus:
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55 --generate_consensus
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56 #end if
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57
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58 #if $filter_ns:
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59 --ns
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60 #end if
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61
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62 -o output
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64 ]]></command>
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65 <inputs>
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66 <param name="forward" type="data" format="fastq" optional="false" label="Forward read" />
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67 <param name="reverse" type="data" format="fastq" optional="true" label="Reverse read" help="Not required."/>
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68 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />
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69 <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." />
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70 <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." />
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71 <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />
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72 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." />
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73 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/>
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74 <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." />
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75 <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." />
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76 <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." />
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77 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." />
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78 <param name="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" />
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79 <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" />
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80 </inputs>
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81 <outputs>
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82 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
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83 <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" />
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84 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" />
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85 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
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86 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
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87 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
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88 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
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89 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="forward" value="forward.fastq" />
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94 <output name="output_coverage">
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95 <assert_contents>
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96 <has_text text="frame: 0" />
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97 <has_text text="1,0" />
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98 <has_text text="948,0" />
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99 </assert_contents>
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100 </output>
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101 <output name="output_dr">
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102 <assert_contents>
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103 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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104 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" />
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105 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" />
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106 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" />
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107 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" />
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108 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" />
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109 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" />
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110 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" />
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111 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" />
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112 </assert_contents>
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113 </output>
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114 <output name="output_hydra">
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115 <assert_contents>
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116 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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117 <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" />
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118 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" />
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119 </assert_contents>
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120 </output>
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121 <output name="output_aa_mt">
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122 <assert_contents>
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123 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
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124 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s101\sP\sPASS\s0.1423\s1574\sWC=aaa;MC=CCa;MCF=0.1423;CAT=NNRTI;SRVL=Yes" />
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125 <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." />
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126 </assert_contents>
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127 </output>
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128 <output name="output_stats">
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129 <assert_contents>
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130 <has_text text="Input Size: 25000"/>
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131 <has_text text="Number of reads filtered due to length: 15074"/>
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132 <has_text text="Number of reads filtered due to average quality score: 501"/>
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133 <has_text text="Number of reads filtered due to presence of Ns: 0"/>
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134 <has_text text="Number of reads filtered due to excess coverage: 0"/>
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135 <has_text text="Number of reads filtered due to poor mapping: 12"/>
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136 <has_text text="Percentage of reads filtered: 62.35"/>
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137 </assert_contents>
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138 </output>
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139 </test>
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140 </tests>
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141 <help><![CDATA[
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142
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143 HyDRA - HIV Drug Resistance Analyzer
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144 ====================================
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145
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146 The HyDRA pipeline provides a pipeline for identifying drug resistance within a Next Generation Sequencing dataset. The pipeline takes as input the raw reads produced by a Next Generation Sequencer and produces a report detailing found drug resistance per sample.
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147
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148 Authors
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149 -------
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150
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151 The HyDRA pipeline was developed by Eric Enns and David Peddle.
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152
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153 Stages
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154 ------
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155
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156 The HyDRA pipleine proceeds through the following stages:
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157
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158 1. Quality Control/Filtering
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159 2. Reference mapping using bowtie2.
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160 3. Variant Calling and filtering using a Poisson distribution.
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161 4. AA Mutation Calling and filtering.
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162 5. Drug Resistance report generation.
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163
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164 Details
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165 -------
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166
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167 The following is an example for running the pipeline, using our included test dataset:
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168 * Output directory name: "/tmp/hydra_out"
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169 * Forward reads: "reads_w_K103N.fastq"
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170
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171 ### Output ###
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172
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173 The detailed output directory tree looks as follows:
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174
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175 /tmp/hydra_out/
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176 * align.bam
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177 * align.bam.bai
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178 * coverage_file.csv
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179 * dr_report.csv
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180 * filtered.fastq
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181 * hydra.vcf
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182 * mutation_report.hmcf
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183 * stats.txt
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184
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185 The description of each of these directories/files are as follows:
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186
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187 * __run.conf__: The configuration used when this output was produced.
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188 * __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq
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189 * __align.bam__: The alignment file in bam format.
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190 * __align.bam.bai__: The index to the alignment file.
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191 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.
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192 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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193 * __filtered.fastq__: The reads remaining after the filtering stage.
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194 * __hydra.vcf__: The variants found by the pipeline.
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195 * __mutation_report.hmcf__: The AA mutations found by the pipeline.
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196 * __stats.txt__: A log file detailing size after filtering and major stages.
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197
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198 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below.
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199
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200 Example: __dr_report.csv__
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201
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202 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
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203 RT,NNRTI,Yes,K,103,N,9.03,155
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204
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205 The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below.
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206
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207 Example: __mutation_report.hmcf__
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208
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209 ##fileformat=HMCFv1
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210 ##fileDate=20150008
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211 ##source=HyDRA
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212 ##reference=/home/ericenns/hydra/var/hxb2_pol.fas
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213 ##INFO=<ID=MC,Number=.,Description="String">
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214 ##INFO=<ID=MCF,Number=.,Description="String">
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215 ##INFO=<ID=WC,Number=.,Description="String">
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216 ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01">
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217 #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO
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218 RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903
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219
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220 ]]></help>
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221 <citations>
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222 </citations>
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223 </tool>