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1 <tool id="hfp_centriflaken_awsbatch" name="centriflaken" version="0.4.2+awsbatch">
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2 <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</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__/0.4.2/cpipes
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39 --pipeline $input_read_type_cond.pipeline_cond.pipeline
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40 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
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41 --fq_single_end true
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42 --flye_genome_size '${genome_size}'
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43 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
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44 --flye_nano_corr true --flye_nano_raw false
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45 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_hq"):
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46 --flye_nano_hq true --flye_nano_raw false
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47 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_raw"):
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48 --flye_pacbio_raw true --flye_nano_raw false
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49 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_corr"):
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50 --flye_pacbio_corr true --flye_nano_raw false
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51 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"):
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52 --flye_pacbio_hifi true --flye_nano_raw false
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53 #end if
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54 #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"):
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55 #if (str($input_read_type_cond.input_read_type) == "single_long"):
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56 --fq_single_end true
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57 #elif (str($input_read_type_cond.input_read_type) == "paired"):
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58 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
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59 #end if
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60 #end if
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61 --input \${input_path}
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62 --output cpipes-output
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63 --fq_suffix '${input_read_type_cond.fq_suffix}'
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64 #if ($fq_filter_by_len != ""):
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65 --fq_filter_by_len $fq_filter_by_len
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66 #end if
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67 --fq_filename_delim '${fq_filename_delim}'
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68 --fq_filename_delim_idx $fq_filename_delim_idx
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69 --centrifuge_extract_bug '${centrifuge_extract_bug}'
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70 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
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71 --seqkit_rmdup_run true
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72 #end if
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73 -profile stdkondagac;
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74 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/CPIPES-Report_multiqc_report.html" "./multiqc_report.html" || exit 1;
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75 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" "kraken2_extract_contigs" || exit 1;
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76 ]]></command>
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77 <inputs>
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78 <conditional name="input_read_type_cond">
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79 <param name="input_read_type" type="select" label="Select the read collection type">
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80 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>
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81 <option value="paired">Paired-End reads</option>
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82 </param>
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83 <when value="single_long">
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84 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
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85 label="Dataset list of unpaired short reads or long reads" />
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86 <conditional name="pipeline_cond">
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87 <param name="pipeline" type="select" label="CPIPES Workflow name"
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88 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for unpaired short reads. Default: centriflaken">
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89 <option value="centriflaken" selected="true">centriflaken</option>
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90 <option value="centriflaken_hy">centriflaken_hy</option>
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91 </param>
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92 <when value="centriflaken">
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93 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type">
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94 <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (<20% error)</option>
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95 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (<3% error)</option>
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96 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
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97 <option value="pacbio_raw">PacBio regular CLR reads (<20% error)</option>
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98 <option value="pacbio_corr">PacBio reads that were corrected with other methods (<3% error)</option>
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99 <option value="pacbio_hifi">PacBio HiFi reads (<1% error)</option>
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100 </param>
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101 <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
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102 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE LONG READS.">
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103 <option value="NA" selected="true">N/A</option>
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104 </param>
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105 </when>
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106 <when value="centriflaken_hy">
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107 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
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108 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
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109 <option value="NA" selected="true">N/A</option>
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110 </param>
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111 <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
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112 help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
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113 <option value="true">yes</option>
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114 <option value="false" selected="true">no</option>
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115 </param>
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116 </when>
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117 </conditional>
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118 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
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119 </when>
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120 <when value="paired">
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121 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
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122 <conditional name="pipeline_cond">
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123 <param name="pipeline" type="select" label="CPIPES Workflow name"
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124 help="Auto selected centriflaken_hy workflow for paired-end short reads.">
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125 <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
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126 </param>
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127 <when value="centriflaken_hy">
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128 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
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129 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
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130 <option value="NA" selected="true">N/A</option>
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131 </param>
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132 <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
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133 help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
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134 <option value="true">yes</option>
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135 <option value="false" selected="true">no</option>
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136 </param>
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137 </when>
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138 </conditional>
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139 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/>
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140 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
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141 </when>
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142 </conditional>
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143 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
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144 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/>
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145 <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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146 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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147 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
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148 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/>
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149 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
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150 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
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151 </param>
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152 <!-- <param name="runtime_profile" type="select" label="Run time profile">
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153 <option value="kondagac" selected="true">conda</option>
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154 <option value="cingularitygac">singularity</option>
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155 </param> -->
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156 </inputs>
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157 <outputs>
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158 <data name="multiqc_report" format="html" label="${input_read_type_cond.pipeline_cond.pipeline}: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
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159 <collection name="assembled_mags" type="list" label="${input_read_type_cond.pipeline_cond.pipeline}: Assembled MAGs on ${on_string}">
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160 <discover_datasets pattern="(?P<name>.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="kraken2_extract_contigs"/>
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161 </collection>
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162 </outputs>
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163 <tests>
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164 <!--Test 01: long reads-->
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165 <test expect_num_outputs="2">
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166 <param name="input">
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167 <collection type="list">
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168 <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
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169 <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
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170 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
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171 </collection>
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172 </param>
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173 <param name="fq_suffix" value=".fastq.gz"/>
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174 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
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175 <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
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176 </test>
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177 </tests>
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178 <help><![CDATA[
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179
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180 .. class:: infomark
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181
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182 **Purpose**
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183
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184 Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These pipelines allow rapid
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185 and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our
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186 previous publication (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172).
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187
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188 ----
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189
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190 .. class:: infomark
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191
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192 **Testing and Validation**
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193
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194 The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs
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195 in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs
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196 of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline.
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197 The Centriflaken pipeline was validated with data from our previously published method (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172) and was able to replicate the detection
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198 and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from
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199 irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was
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200 done on the command line on the CFSAN Raven2 HPC Cluster.
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201
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202
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203 ----
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204
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205 .. class:: infomark
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206
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207 **Outputs**
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208
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209 The main output files are:
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210
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211 ::
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212
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213 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
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214 Please note that due to MultiQC customizations, the preview (eye icon) will not
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215 work within Galaxy for the MultiQC report. Please download the file by clicking
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216 on the floppy icon and view it in your browser on your local desktop/workstation.
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217 - Final assembly: contains contigs and possibly scaffolds.
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218
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219 ]]></help>
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220 <citations>
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221 <citation type="bibtex">
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222 @misc{gitlabCPIPES,
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223 author = {Konganti, Kranti},
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224 year = {2022},
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225 title = {CPIPES - Centriflaken},
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226 publisher = {GitLab},
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227 journal = {GitLab repository},
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228 url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes}}
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229 </citation>
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230 </citations>
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231 </tool>
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