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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 disable_version_detection: true
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18 report_section_order:
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19 BETTERCALLSAL_SALMON_COUNTS:
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20 order: -897
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21 BETTERCALLSAL_SALYN_collated_table:
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22 order: -898
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23 BETTERCALLSAL_collated_table:
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24 order: -899
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25 BCS_SOURMASH_MATRIX_collated_table:
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26 order: -900
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27 MLST_collated_table:
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28 order: -991
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29 ABRICATE_NCBIAMRPLUS_collated_table:
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30 order: -992
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31 ABRICATE_MEGARES_collated_table:
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32 order: -993
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33 ABRICATE_RESFINDER_collated_table:
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34 order: -994
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35 ABRICATE_ARGANNOT_collated_table:
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36 order: -995
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37 filtlong:
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38 order: -996
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39 fastqc:
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40 order: -997
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41 fastqc-1:
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42 order: -998
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43 software_versions:
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44 order: -999
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45
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46 export_plots: true
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47
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48 # Run only these modules
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49 run_modules:
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50 - filtlong
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51 - fastqc
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52 - custom_content
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53
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54 module_order:
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55 - filtlong:
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56 name: "filtlong"
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57 info: >
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58 section of the report shows read statistics <b>before</b> and <b>after</b> quality trimming
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59 with <code>filtlong</code> on raw long reads.
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60 path_filters:
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61 - "*.filtlong.log"
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62 - fastqc:
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63 name: "FastQC (Raw reads)"
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64 info: >
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65 section of the report shows FastQC results <b>before</b> quality control
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66 on long reads.
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67 path_filters:
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68 - "*.raw_fastqc.zip"
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69 - fastqc:
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70 name: "FastQC (Filtered reads)"
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71 info: >
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72 section of the report shows FastQC results <b>after</b> quality control
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73 on long reads.
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74 path_filters:
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75 - "*.filtered_fastqc.zip"
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