Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/conf/multiqc/nowayout_mqc.yml @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 title: CPIPES Report |
| kkonganti@0 | 2 intro_text: > |
| kkonganti@0 | 3 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. |
| kkonganti@0 | 4 report_comment: > |
| kkonganti@0 | 5 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 | 6 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory. |
| kkonganti@0 | 7 report_header_info: |
| kkonganti@0 | 8 - CPIPES Version: CPIPES_Version_Placeholder |
| kkonganti@0 | 9 - Workflow: Workflow_Name_Placeholder |
| kkonganti@0 | 10 - Workflow Version: Workflow_Version_Placeholder |
| kkonganti@0 | 11 - Conceived By: "Kranti Konganti" |
| kkonganti@0 | 12 - Input Directory: Workflow_Input_Placeholder |
| kkonganti@0 | 13 - Output Directory: Workflow_Output_Placeholder |
| kkonganti@0 | 14 show_analysis_paths: False |
| kkonganti@0 | 15 show_analysis_time: False |
| kkonganti@0 | 16 disable_version_detection: true |
| kkonganti@0 | 17 report_section_order: |
| kkonganti@0 | 18 kraken: |
| kkonganti@0 | 19 order: -994 |
| kkonganti@0 | 20 NOWAYOUT_collated_table: |
| kkonganti@0 | 21 order: -995 |
| kkonganti@0 | 22 NOWAYOUT_INDIV_READS_MAPPED_collated_table: |
| kkonganti@0 | 23 order: -996 |
| kkonganti@0 | 24 fastp: |
| kkonganti@0 | 25 order: -997 |
| kkonganti@0 | 26 fastqc: |
| kkonganti@0 | 27 order: -998 |
| kkonganti@0 | 28 software_versions: |
| kkonganti@0 | 29 order: -999 |
| kkonganti@0 | 30 |
| kkonganti@0 | 31 export_plots: true |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 # Run only these modules |
| kkonganti@0 | 34 run_modules: |
| kkonganti@0 | 35 - fastqc |
| kkonganti@0 | 36 - fastp |
| kkonganti@0 | 37 - kraken |
| kkonganti@0 | 38 - custom_content |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 module_order: |
| kkonganti@0 | 41 - kraken: |
| kkonganti@0 | 42 name: "SOURMASH TAX METAGENOME" |
| kkonganti@0 | 43 href: "https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results" |
| kkonganti@0 | 44 doi: "10.21105/joss.00027" |
| kkonganti@0 | 45 info: > |
| kkonganti@0 | 46 section of the report shows how <b>reads</b> are approximately classified. |
| kkonganti@0 | 47 Please note that the plot title below is shown as |
| kkonganti@0 | 48 <b>Kraken2: Top taxa</b> since <code>kreport</code> fornat was used |
| kkonganti@0 | 49 to create Kraken-style reports with <code>sourmash tax metagenome</code>. |
| kkonganti@0 | 50 path_filters: |
| kkonganti@0 | 51 - "*.kreport.txt" |
| kkonganti@0 | 52 - fastqc: |
| kkonganti@0 | 53 name: "FastQC" |
| kkonganti@0 | 54 info: > |
| kkonganti@0 | 55 section of the report shows FastQC results <b>before</b> adapter trimming |
| kkonganti@0 | 56 on SE reads or on merged PE reads. |
| kkonganti@0 | 57 path_filters: |
| kkonganti@0 | 58 - "*_fastqc.zip" |
| kkonganti@0 | 59 - fastp: |
| kkonganti@0 | 60 name: "fastp" |
| kkonganti@0 | 61 info: > |
| kkonganti@0 | 62 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming |
| kkonganti@0 | 63 with <code>fastp</code> on SE reads or on merged PE reads. |
| kkonganti@0 | 64 path_filters: |
| kkonganti@0 | 65 - "*.fastp.json" |