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/sequoia/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: disable_version_detection: true
kkonganti@0: report_section_order:
kkonganti@0:     kraken:
kkonganti@0:         order: -994
kkonganti@0:     NOWAYOUT_collated_table:
kkonganti@0:         order: -995
kkonganti@0:     NOWAYOUT_INDIV_READS_MAPPED_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:     - fastqc
kkonganti@0:     - fastp
kkonganti@0:     - kraken
kkonganti@0:     - custom_content
kkonganti@0: 
kkonganti@0: module_order:
kkonganti@0:     - kraken:
kkonganti@0:           name: "SOURMASH TAX METAGENOME"
kkonganti@0:           href: "https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results"
kkonganti@0:           doi: "10.21105/joss.00027"
kkonganti@0:           info: >
kkonganti@0:               section of the report shows how <b>reads</b> are approximately classified.
kkonganti@0:               Please note that the plot title below is shown as
kkonganti@0:               <b>Kraken2: Top taxa</b> since <code>kreport</code> fornat was used
kkonganti@0:               to create Kraken-style reports with <code>sourmash tax metagenome</code>.
kkonganti@0:           path_filters:
kkonganti@0:               - "*.kreport.txt"
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 reads or on merged PE reads.
kkonganti@0:           path_filters:
kkonganti@0:               - "*_fastqc.zip"
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 reads or on merged PE reads.
kkonganti@0:           path_filters:
kkonganti@0:               - "*.fastp.json"