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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/bettercallsal/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 skip_versions_section: True
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17 report_section_order:
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18 BETTERCALLSAL_SALMON_COUNTS:
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19 order: -898
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20 BETTERCALLSAL_SALYN_collated_table:
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21 order: -899
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22 BETTERCALLSAL_collated_table:
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23 order: -900
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24 BCS_SOURMASH_MATRIX_collated_table:
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25 order: -991
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26 MLST_collated_table:
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27 order: -992
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28 ABRICATE_NCBIAMRPLUS_collated_table:
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29 order: -993
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30 ABRICATE_MEGARES_collated_table:
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31 order: -994
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32 ABRICATE_RESFINDER_collated_table:
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33 order: -995
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34 ABRICATE_ARGANNOT_collated_table:
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35 order: -996
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36 fastp:
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37 order: -997
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38 fastqc:
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39 order: -998
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40 software_versions:
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41 order: -999
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42
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43 export_plots: true
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44
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45 # Run only these modules
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46 run_modules:
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47 - fastp
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48 - fastqc
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49 - custom_content
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50
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51 module_order:
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52 - fastp:
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53 name: "fastp"
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54 info: >
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55 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
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56 with <code>fastp</code> on SE, merged PE or concatenated PE reads.
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57 path_filters:
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58 - "*.fastp.json"
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59 - fastqc:
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60 name: "FastQC"
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61 info: >
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62 section of the report shows FastQC results <b>before</b> adapter trimming
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63 on SE, merged PE or concatenated PE reads.
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64 path_filters:
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65 - "*_fastqc.zip"
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