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1 custom_logo: "FDa-Logo-Blue---medium-01.png"
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2 custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan"
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3 custom_logo_title: "CFSAN, FDA"
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4 title: CPIPES Report
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5 intro_text: >
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6 CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2.
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7 report_comment: >
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8 This report has been generated by the <a href="https://cfsan-git.fda.gov/Kranti.Konganti/cpipes/blob/master/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
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9 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
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10 report_header_info:
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11 - CPIPES Version: CPIPES_Version_Placeholder
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12 - Workflow: Workflow_Name_Placeholder
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13 - Workflow Version: Workflow_Version_Placeholder
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14 - Input Directory: Workflow_Input_Placeholder
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15 - Output Directory: Workflow_Output_Placeholder
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16 - Developer E-mail: "Kranti.Konganti@fda.hhs.gov"
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17 - Stakeholder E-mail: "Narjol.Gonzalez-Escalona@fda.hhs.gov"
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18 show_analysis_paths: False
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19 show_analysis_time: False
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20 report_section_order:
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21 MLST_collated_table:
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22 order: -989
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23 ECTYPER_collated_table:
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24 order: -990
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25 SEROTYPEFINDER_collated_table:
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26 order: -991
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27 SEQSERO2_collated_table:
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28 order: -992
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29 ABRICATE_ECOLI_VF_collated_table:
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30 order: -993
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31 ABRICATE_NCBI_collated_table:
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32 order: -994
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33 ABRICATE_NCBIAMRPLUS_collated_table:
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34 order: -995
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35 ABRICATE_MEGARES_collated_table:
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36 order: -996
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37 ABRICATE_RESFINDER_collated_table:
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38 order: -997
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39 ABRICATE_ARGANNOT_collated_table:
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40 order: -998
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41 software_versions:
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42 order: -999
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43
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44 export_plots: true
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45
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46 # Run only these modules
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47 run_modules:
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48 - fastqc
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49 - kraken
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50 - custom_content
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51
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52 module_order:
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53 - fastqc:
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54 name: "FastQC"
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55 info: "section of the report shows FastQC results <b>before</b> adapter trimming."
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56 path_filters:
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57 - "*_fastqc.zip"
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58 - kraken:
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59 name: "Centrifuge"
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60 href: "https://ccb.jhu.edu/software/centrifuge"
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61 doi: "10.1101/gr.210641.116"
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62 info: >
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63 section of the report shows how <b>reads</b> are classified.
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64 Please note that the plot title below is shown as
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65 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
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66 to create Kraken-style reports from centrifuge output files.
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67 path_filters:
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68 - "*.kreport.txt"
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69 - kraken:
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70 name: "Kraken2"
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71 info: "section of the report shows how <b>assembled contigs</b> are classified."
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72 path_filters:
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73 - "*.report.txt"
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74
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75 extra_fn_clean_exts:
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76 - ".centrifuge.kreport"
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77 - ".report"
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78
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79 table_columns_visible:
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80 Kraken: False
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81 Kraken2: False
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82 Centrifuge: False
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