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1 <tool id="hfp_nowayout_awsbatch" name="nowayout" version="0.5.0+awsbatch">
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2 <description>An automated workflow to identify Mitochondrial reads and classify Eukaryotes.</description>
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3 <requirements>
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4 <container type="docker">quay.io/galaxytrakr/mulled-v2-ebd88135862aa647eeae73d4d8e6ea8ec81245cd:v5.0</container>
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5 </requirements>
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6 <version_command>nextflow -version</version_command>
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7 <command detect_errors="exit_code"><![CDATA[
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8 export MAMBA_ROOT_PREFIX="/server/galaxy/data/nextflow-micromamba-cache";
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9 export NXF_HOME=\$(pwd)"/.nextflow-home";
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10 input_path=\$(pwd)"/cpipes-input";
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11 mkdir -p "\${input_path}" || exit 1;
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12 #import re
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13 #if (str($input_read_type_cond.input_read_type) == "single_long"):
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14 #for _, $unpaired in enumerate($input_read_type_cond.input):
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15 #set read1 = str($unpaired.name)
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16 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
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17 #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext))
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18 #set read1 = str($unpaired.name) + str('.') + $read1_ext
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19 #end if
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20 ln -sf '$unpaired' "\${input_path}/$read1";
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21 #end for
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22 #elif (str($input_read_type_cond.input_read_type) == "paired"):
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23 #for _, $pair in enumerate($input_read_type_cond.input_pair)
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24 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
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25 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
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26 #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext))
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27 #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext))
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28 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
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29 #set read_R1 = $read_R1 + str('.') + $read_R1_ext
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30 #end if
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31 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
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32 #set read_R2 = $read_R2 + str('.') + $read_R2_ext
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33 #end if
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34 ln -sf '$pair.forward' "\${input_path}/$read_R1";
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35 ln -sf '$pair.reverse' "\${input_path}/$read_R2";
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36 #end for
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37 #end if
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38 $__tool_directory__/0.5.0/cpipes
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39 --pipeline nowayout
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40 --input \${input_path}
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41 --output cpipes-output
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42 --fq_suffix '${input_read_type_cond.fq_suffix}'
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43 #if (str($input_read_type_cond.input_read_type) == "single_long"):
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44 --fq_single_end true
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45 #elif (str($input_read_type_cond.input_read_type) == "paired"):
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46 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
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47 #end if
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48 --db_mode $nowo_db_mode
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49 --nowo_thresholds $nowo_thresholds
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50 --fq_filename_delim '${fq_filename_delim}'
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51 --fq_filename_delim_idx $fq_filename_delim_idx
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52 -profile stdkondagac;
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53 mv './cpipes-output/nowayout-multiqc/CPIPES-Report_multiqc_report.html' './multiqc_report.html' || exit 1;
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54 if [ -e './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' ]; then mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' './CPIPES_nowayout_krona.html'; else echo '<html><h1>No mitochondrial reads detected in any of the samples</h1></html>' > './CPIPES_nowayout_krona.html'; fi;
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55 rm -rf ./cpipes-output || exit 1;
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56 rm -rf ./work || exit 1;
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57 ]]></command>
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58 <inputs>
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59 <conditional name="input_read_type_cond">
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60 <param name="input_read_type" type="select" label="Select the read collection type">
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61 <option value="single_long" selected="true">Single-End short reads</option>
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62 <option value="paired">Paired-End short reads</option>
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63 </param>
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64 <when value="single_long">
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65 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
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66 label="Dataset list of unpaired short reads or long reads" />
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67 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Single-End FASTQ"/>
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68 </when>
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69 <when value="paired">
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70 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
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71 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"
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72 help="For any data sets downloaded from NCBI into Galaxy, change this to _forward.fastq.gz suffix."/>
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73 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"
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74 help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
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75 </when>
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76 </conditional>
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77 <param name="nowo_db_mode" type="select" label="Select the database with nowayout"
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78 help="Please see below about different databases.">
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79 <option value="mitomine2" selected="true">mitomine2</option>
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80 <option value="mitomine">mitomine</option>
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81 <option value="cytox1">cytox1</option>
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82 <option value="voucher">voucher</option>
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83 <option value="ganoderma">ganoderma</option>
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84 <option value="listeria">listeria</option>
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85 </param>
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86 <param name="nowo_thresholds" type="select" label="Enter the type of base quality thresholds to be set with nowayout"
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87 help="The default value sets strictest thresholds that tends to filter out most of the false positive hits.">
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88 <option value="strict" selected="true">strict</option>
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89 <option value="relax">relax</option>
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90 </param>
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91 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
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92 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
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93 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
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94 </inputs>
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95 <outputs>
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96 <data name="krona_chart" format="html" label="nowayout: Krona Chart on ${on_string}" from_work_dir="CPIPES_nowayout_krona.html"/>
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97 <data name="multiqc_report" format="html" label="nowayout: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
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98 </outputs>
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99 <tests>
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100 <!--Test 01: long reads-->
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101 <test expect_num_outputs="2">
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102 <param name="input">
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103 <collection type="list">
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104 <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
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105 <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
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106 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
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107 </collection>
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108 </param>
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109 <param name="fq_suffix" value=".fastq.gz"/>
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110 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
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111 <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115
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116 .. class:: infomark
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117
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118 **Purpose**
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119
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120 nowayout is a mitochondrial metagenomics classifier for Eukaryotes.
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121 It uses a custom kma database to identify mitochondrial reads and
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122 performs read classification followed by further read classification
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123 reinforcement using sourmash.
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124
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125 It is written in Nextflow and is part of the modular data analysis pipelines (CFSAN PIPELINES or CPIPES for short) at HFP.
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126
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127
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128 ----
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129
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130 .. class:: infomark
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131
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132 **Databases**
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133
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134 - *mitomine2*: Big database that works in almost all scenarios.
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135 - *cytox1*: Collection of only non-redundant COXI genes from NCBI.
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136 - *voucher*: Collection of only non-redundant voucher sequences from NCBI.
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137 - *ganoderma*: Collection of only non-redundant mtDNA sequences of Ganoderma fungi.
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138 - *listeria*: Collection of organelle sequences and other rRNA genes for Listeria.
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139
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140
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141 ----
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142
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143 .. class:: infomark
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144
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145 **Testing and Validation**
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146
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147 The CPIPES - nowayout Nextflow pipeline has been wrapped to make it work in Galaxy.
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148 It takes in either paired or unpaired short reads list as an input and generates a MultiQC report
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149 which contains relative abundances in context of number of mitochondrial reads identified. It also
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150 generates a Krona chart for each sample. The pipeline has been tested on multiple internal insect
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151 mixture samples. All the original testing and validation was done on the command line on the
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152 HFP Reedling HPC Cluster.
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153
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154
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155 ----
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156
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157 .. class:: infomark
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158
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159 **Please note**
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160
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161 - *nowayout* only works on Illumina short reads (paired or unpaired).
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162 - *nowayout* uses a custom kma database named *mitomine*.
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163 - The custom database will be incrementally augmented and refined over time.
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164 - *mitomine* stats:
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165 - Contains ~ 2.93M non-redundant mitochondrial and voucher sequences.
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166 - Represents ~ 717K unique species.
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167 - Other databases are also available but will be seldom updated.
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168
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169 ----
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170
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171 .. class:: infomark
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172
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173 **Outputs**
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174
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175 The main output file is a:
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176
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177 ::
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178
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179 - MultiQC Report: Contains a brief summary report including individual Mitochondrial reads identified
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180 per sample and relative abundances in context of the total number of Mitochondrial reads
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181 identified.
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182
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183 Please note that due to MultiQC customizations, the preview (eye icon) will not
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184 work within Galaxy for the MultiQC report. Please download the file by clicking
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185 on the floppy icon and view it in your browser on your local desktop/workstation.
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186 You can export the tables and plots from the downloaded MultiQC report.
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187
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188 ]]></help>
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189 <citations>
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190 <citation type="bibtex">
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191 @article{nowayout,
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192 author = {Konganti, Kranti},
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193 year = {2025},
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194 month = {May},
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195 title = {nowayout: An automated mitrochiondrial read classifier for Eukaryotes.},
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196 journal = {Manuscript in preparation},
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197 doi = {10.3389/xxxxxxxxxxxxxxxxxx},
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198 url = {https://xxxxxxx/articles/10.3389/xxxxxxxxxxxx/full}}
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199 </citation>
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200 </citations>
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201 </tool>
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