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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/sequoia/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 disable_version_detection: true
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17 report_section_order:
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18 kraken:
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19 order: -994
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20 NOWAYOUT_collated_table:
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21 order: -995
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22 NOWAYOUT_INDIV_READS_MAPPED_collated_table:
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23 order: -996
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24 fastp:
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25 order: -997
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26 fastqc:
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27 order: -998
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28 software_versions:
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29 order: -999
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30
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31 export_plots: true
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32
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33 # Run only these modules
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34 run_modules:
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35 - fastqc
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36 - fastp
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37 - kraken
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38 - custom_content
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39
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40 module_order:
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41 - kraken:
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42 name: "SOURMASH TAX METAGENOME"
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43 href: "https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results"
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44 doi: "10.21105/joss.00027"
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45 info: >
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46 section of the report shows how <b>reads</b> are approximately classified.
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47 Please note that the plot title below is shown as
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48 <b>Kraken2: Top taxa</b> since <code>kreport</code> fornat was used
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49 to create Kraken-style reports with <code>sourmash tax metagenome</code>.
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50 path_filters:
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51 - "*.kreport.txt"
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52 - fastqc:
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53 name: "FastQC"
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54 info: >
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55 section of the report shows FastQC results <b>before</b> adapter trimming
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56 on SE reads or on merged PE reads.
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57 path_filters:
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58 - "*_fastqc.zip"
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59 - fastp:
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60 name: "fastp"
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61 info: >
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62 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
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63 with <code>fastp</code> on SE reads or on merged PE reads.
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64 path_filters:
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65 - "*.fastp.json"
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