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1 title: CPIPES Report
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2 intro_text: >
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3 CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2.
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4 report_comment: >
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5 This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/centriflaken" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
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6 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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7 report_header_info:
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8 - CPIPES Version: CPIPES_Version_Placeholder
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9 - Workflow: Workflow_Name_Placeholder
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10 - Workflow Version: Workflow_Version_Placeholder
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11 - Input Directory: Workflow_Input_Placeholder
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12 - Output Directory: Workflow_Output_Placeholder
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13 show_analysis_paths: False
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14 show_analysis_time: False
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15 report_section_order:
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16 MLST_collated_table:
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17 order: -989
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18 ECTYPER_collated_table:
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19 order: -990
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20 SEROTYPEFINDER_collated_table:
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21 order: -991
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22 SEQSERO2_collated_table:
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23 order: -992
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24 ABRICATE_ECOLI_VF_collated_table:
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25 order: -993
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26 ABRICATE_NCBI_collated_table:
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27 order: -994
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28 ABRICATE_NCBIAMRPLUS_collated_table:
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29 order: -995
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30 ABRICATE_MEGARES_collated_table:
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31 order: -996
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32 ABRICATE_RESFINDER_collated_table:
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33 order: -997
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34 ABRICATE_ARGANNOT_collated_table:
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35 order: -998
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36 software_versions:
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37 order: -999
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38
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39 export_plots: true
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40
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41 # Run only these modules
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42 run_modules:
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43 - fastqc
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44 - kraken
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45 - custom_content
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46
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47 module_order:
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48 - fastqc:
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49 name: "FastQC"
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50 info: "section of the report shows FastQC results <b>before</b> adapter trimming."
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51 path_filters:
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52 - "*_fastqc.zip"
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53 - kraken:
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54 name: "Centrifuge"
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55 href: "https://ccb.jhu.edu/software/centrifuge"
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56 doi: "10.1101/gr.210641.116"
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57 info: >
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58 section of the report shows how <b>reads</b> are classified.
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59 Please note that the plot title below is shown as
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60 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
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61 to create Kraken-style reports from centrifuge output files.
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62 path_filters:
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63 - "*.kreport.txt"
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64 - kraken:
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65 name: "Kraken2"
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66 info: "section of the report shows how <b>assembled contigs</b> are classified."
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67 path_filters:
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68 - "*.report.txt"
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69
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70 extra_fn_clean_exts:
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71 - ".centrifuge.kreport"
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72 - ".report"
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73
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74 table_columns_visible:
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75 Kraken: False
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76 Kraken2: False
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77 Centrifuge: False
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