kkonganti@11: title: CPIPES Report
kkonganti@11: intro_text: >
kkonganti@11:     CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. 
kkonganti@11: report_comment: >
kkonganti@11:     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>
kkonganti@11:     analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
kkonganti@11: report_header_info:
kkonganti@11:     - CPIPES Version: CPIPES_Version_Placeholder
kkonganti@11:     - Workflow: Workflow_Name_Placeholder
kkonganti@11:     - Workflow Version: Workflow_Version_Placeholder
kkonganti@11:     - Conceived By: 'Kranti Konganti'
kkonganti@11:     - Input Directory: Workflow_Input_Placeholder
kkonganti@11:     - Output Directory: Workflow_Output_Placeholder
kkonganti@11: show_analysis_paths: False
kkonganti@11: show_analysis_time: False
kkonganti@11: report_section_order:
kkonganti@11:     BETTERCALLSAL_SALMON_COUNTS:
kkonganti@11:         order: -898
kkonganti@11:     BETTERCALLSAL_SALYN_collated_table:
kkonganti@11:         order: -899
kkonganti@11:     BETTERCALLSAL_collated_table:
kkonganti@11:         order: -900
kkonganti@11:     BCS_SOURMASH_MATRIX_collated_table:
kkonganti@11:         order: -991
kkonganti@11:     MLST_collated_table:
kkonganti@11:         order: -992
kkonganti@11:     ABRICATE_NCBIAMRPLUS_collated_table:
kkonganti@11:         order: -993
kkonganti@11:     ABRICATE_MEGARES_collated_table:
kkonganti@11:         order: -994
kkonganti@11:     ABRICATE_RESFINDER_collated_table:
kkonganti@11:         order: -995
kkonganti@11:     ABRICATE_ARGANNOT_collated_table:
kkonganti@11:         order: -996
kkonganti@11:     fastp:
kkonganti@11:         order: -997
kkonganti@11:     fastqc:
kkonganti@11:         order: -998
kkonganti@11:     software_versions:
kkonganti@11:         order: -999
kkonganti@11: 
kkonganti@11: export_plots: true
kkonganti@11: 
kkonganti@11: # Run only these modules
kkonganti@11: run_modules:
kkonganti@11:     - fastp
kkonganti@11:     - fastqc
kkonganti@11:     - custom_content
kkonganti@11: 
kkonganti@11: module_order:
kkonganti@11:     - fastp:
kkonganti@11:         name: 'fastp'
kkonganti@11:         info: >
kkonganti@11:             section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
kkonganti@11:             with <code>fastp</code> on SE, merged PE or concatenated PE reads.
kkonganti@11:         path_filters:
kkonganti@11:             - '*.fastp.json'
kkonganti@11:     - fastqc:
kkonganti@11:         name: 'FastQC'
kkonganti@11:         info: >
kkonganti@11:             section of the report shows FastQC results <b>before</b> adapter trimming
kkonganti@11:             on SE, merged PE or concatenated PE reads.
kkonganti@11:         path_filters:
kkonganti@11:             - '*_fastqc.zip'