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1 <tool id="cfsan_centriflaken" name="Centriflaken" version="0.2.0+galaxy0">
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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 <requirement type="package" version="22.04">nextflow</requirement>
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5 <requirement type="package">graphviz</requirement>
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6 </requirements>
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7 <version_command>nextflow -version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mkdir -p cpipes-input;
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10 #for $key in $input.keys()
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11 ln -sf '$input[$key]' './cpipes-input/$key';
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12 #end for
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13 pwd_path=\$(pwd);
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14 $__tool_directory__/0.2.1/cpipes
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15 #if ($pipeline == "centriflaken"):
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16 --pipeline $pipeline
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17 --fq_single_end true
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18 #elif ($pipeline == "centriflaken_hy"):
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19 --pipeline $pipeline
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20 #if ($reads_lib_layout == "single"):
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21 --fq_single_end true
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22 #else:
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23 --fq_single_end false
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24 #end if
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25 #end if
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26 --input \${pwd_path}/cpipes-input
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27 --output \${pwd_path}/cpipes-output
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28 --fq_suffix '${fq_suffix}'
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29 --fq_filename_delim '${fq_filename_delim}'
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30 --fq_filename_delim_idx $fq_filename_delim_idx
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31 --centrifuge_extract_bug '${centrifuge_extract_bug}'
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32 --flye_genome_size '${genome_size}'
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33 -profile $runtime_profile
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34 -resume;
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35 cp \${pwd_path}/cpipes-output/${pipeline}-multiqc/multiqc_report.html ${pwd_path}/;
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36 ]]></command>
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37 <inputs>
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38 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
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39 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken"
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40 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
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41 <option value="centriflaken">centriflaken</option>
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42 <option value="centriflaken_hy">centriflaken_hy</option>
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43 </param>
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44 <param name="read_lib_layout" type="select" label="Short Read Library Layout" value="single"
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45 help="If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End">
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46 <option value="single">Single-End</option>
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47 <option value="paired">Paired-End</option>
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48 </param>
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49 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
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50 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
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51 <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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52 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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53 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
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54 <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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55 <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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56 <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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57 </param>
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58 <param name="runtime_profile" type="select" label="Run time profile" value="kondagac">
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59 <option value="kondagac">conda</option>
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60 <option value="cingularitygac">singularity</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
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65 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
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66 <discover_datasets pattern="(?P<name>.*)\.assembly_filtered_contigs\.fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
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67 </collection>
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68 </outputs>
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69 <tests>
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70 <!--Test 01: long reads-->
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71 <test expect_num_outputs="2">
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72 <param name="input">
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73 <collection type="list">
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74 <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
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75 <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
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76 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
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77 </collection>
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78 </param>
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79 <param name="fq_suffix" value=".fastq.gz"/>
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80 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
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81 <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85
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86 .. class:: infomark
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87
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88 **Purpose**
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89
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90 Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These piepelines allow rapid
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91 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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92 previous publication (https://doi.org/10.1371/journal.pone.0245172).
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93
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94 ----
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95
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96 .. class:: infomark
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97
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98 **Testing and Validation**
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99
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100 The 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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101 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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102 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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103 The Centriflaken pipeline was validated with data from our previously published method (Maguire et al, 2021) and was able to replicate the detection
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104 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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105 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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106 done on the command line on the CFSAN Raven2 HPC Cluster.
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107
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108
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109 ----
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110
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111 .. class:: infomark
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112
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113 **Outputs**
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114
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115 The main output files are:
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116
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117 ::
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118
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119 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
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120 - Final assembly: contains contigs and possibly scaffolds (see below).
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121
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122 ]]></help>
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123 <citations>
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124 <citation type="bibtex">
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125 @misc{gitlabCPIPES,
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126 author = {Konganti, Kranti},
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127 year = {2022},
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128 title = {CPIPES - Centriflaken},
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129 publisher = {GitLab},
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130 journal = {GitLab repository},
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131 url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes}}
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132 </citation>
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133 </citations>
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134 </tool>
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