kkonganti@0: title: CPIPES Report
kkonganti@0: intro_text: >
kkonganti@0:     CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. 
kkonganti@0: report_comment: >
kkonganti@0:     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>
kkonganti@0:     analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
kkonganti@0: report_header_info:
kkonganti@0:     - CPIPES Version: CPIPES_Version_Placeholder
kkonganti@0:     - Workflow: Workflow_Name_Placeholder
kkonganti@0:     - Workflow Version: Workflow_Version_Placeholder
kkonganti@0:     - Conceived By: 'Kranti Konganti'
kkonganti@0:     - Input Directory: Workflow_Input_Placeholder
kkonganti@0:     - Output Directory: Workflow_Output_Placeholder
kkonganti@0: show_analysis_paths: False
kkonganti@0: show_analysis_time: False
kkonganti@0: report_section_order:
kkonganti@0:     MLST_collated_table:
kkonganti@0:         order: -989
kkonganti@0:     RMLST_collated_table:
kkonganti@0:         order: -990
kkonganti@0:     prokka:
kkonganti@0:         order: -991
kkonganti@0:     quast:
kkonganti@0:         order: -992
kkonganti@0:     ABRICATE_NCBIAMRPLUS_collated_table:
kkonganti@0:         order: -993
kkonganti@0:     ABRICATE_MEGARES_collated_table:
kkonganti@0:         order: -994
kkonganti@0:     ABRICATE_RESFINDER_collated_table:
kkonganti@0:         order: -995
kkonganti@0:     ABRICATE_ARGANNOT_collated_table:
kkonganti@0:         order: -996
kkonganti@0:     fastp:
kkonganti@0:         order: -997
kkonganti@0:     fastqc:
kkonganti@0:         order: -998
kkonganti@0:     software_versions:
kkonganti@0:         order: -999
kkonganti@0: 
kkonganti@0: export_plots: true
kkonganti@0: 
kkonganti@0: # Run only these modules
kkonganti@0: run_modules:
kkonganti@0:     - fastp
kkonganti@0:     - fastqc
kkonganti@0:     - prokka
kkonganti@0:     - quast
kkonganti@0:     - custom_content
kkonganti@0: 
kkonganti@0: module_order:
kkonganti@0:     - fastp:
kkonganti@0:         name: 'fastp'
kkonganti@0:         info: >
kkonganti@0:             section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
kkonganti@0:             with <code>fastp</code> on SE, merged PE or concatenated PE reads.
kkonganti@0:         path_filters:
kkonganti@0:             - '*.fastp.json'
kkonganti@0:     - fastqc:
kkonganti@0:         name: 'FastQC'
kkonganti@0:         info: >
kkonganti@0:             section of the report shows FastQC results <b>before</b> adapter trimming
kkonganti@0:             on SE, merged PE or concatenated PE reads.
kkonganti@0:         path_filters:
kkonganti@0:             - '*_fastqc.zip'
kkonganti@0: 
kkonganti@0: # Custom module config
kkonganti@0: prokka_table: true
kkonganti@0: