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1 title: CPIPES Report
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2 intro_text: >
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3 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, 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/cronology/blob/master/readme/Workflow_Name_Placeholder.md" 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 - Conceived By: 'Kranti Konganti'
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12 - Input Directory: Workflow_Input_Placeholder
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13 - Output Directory: Workflow_Output_Placeholder
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14 show_analysis_paths: False
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15 show_analysis_time: False
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16 report_section_order:
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17 MLST_collated_table:
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18 order: -989
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19 RMLST_collated_table:
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20 order: -990
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21 prokka:
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22 order: -991
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23 quast:
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24 order: -992
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25 ABRICATE_NCBIAMRPLUS_collated_table:
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26 order: -993
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27 ABRICATE_MEGARES_collated_table:
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28 order: -994
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29 ABRICATE_RESFINDER_collated_table:
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30 order: -995
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31 ABRICATE_ARGANNOT_collated_table:
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32 order: -996
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33 fastp:
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34 order: -997
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35 fastqc:
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36 order: -998
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37 software_versions:
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38 order: -999
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39
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40 export_plots: true
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41
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42 # Run only these modules
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43 run_modules:
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44 - fastp
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45 - fastqc
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46 - prokka
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47 - quast
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48 - custom_content
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49
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50 module_order:
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51 - fastp:
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52 name: 'fastp'
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53 info: >
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54 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
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55 with <code>fastp</code> on SE, merged PE or concatenated PE reads.
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56 path_filters:
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57 - '*.fastp.json'
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58 - fastqc:
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59 name: 'FastQC'
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60 info: >
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61 section of the report shows FastQC results <b>before</b> adapter trimming
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62 on SE, merged PE or concatenated PE reads.
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63 path_filters:
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64 - '*_fastqc.zip'
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65
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66 # Custom module config
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67 prokka_table: true
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68
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