Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/conf/multiqc/bettercallsal_mqc.yml @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 title: CPIPES Report |
| kkonganti@1 | 2 intro_text: > |
| kkonganti@1 | 3 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. |
| kkonganti@1 | 4 report_comment: > |
| kkonganti@1 | 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> |
| kkonganti@1 | 6 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory. |
| kkonganti@1 | 7 report_header_info: |
| kkonganti@1 | 8 - CPIPES Version: CPIPES_Version_Placeholder |
| kkonganti@1 | 9 - Workflow: Workflow_Name_Placeholder |
| kkonganti@1 | 10 - Workflow Version: Workflow_Version_Placeholder |
| kkonganti@1 | 11 - Conceived By: 'Kranti Konganti' |
| kkonganti@1 | 12 - Input Directory: Workflow_Input_Placeholder |
| kkonganti@1 | 13 - Output Directory: Workflow_Output_Placeholder |
| kkonganti@1 | 14 show_analysis_paths: False |
| kkonganti@1 | 15 show_analysis_time: False |
| kkonganti@1 | 16 report_section_order: |
| kkonganti@1 | 17 BETTERCALLSAL_SALMON_COUNTS: |
| kkonganti@1 | 18 order: -993 |
| kkonganti@1 | 19 BETTERCALLSAL_SALYN_collated_table: |
| kkonganti@1 | 20 order: -994 |
| kkonganti@1 | 21 BETTERCALLSAL_collated_table: |
| kkonganti@1 | 22 order: -995 |
| kkonganti@1 | 23 BCS_SOURMASH_MATRIX_collated_table: |
| kkonganti@1 | 24 order: -996 |
| kkonganti@1 | 25 fastp: |
| kkonganti@1 | 26 order: -997 |
| kkonganti@1 | 27 fastqc: |
| kkonganti@1 | 28 order: -998 |
| kkonganti@1 | 29 software_versions: |
| kkonganti@1 | 30 order: -999 |
| kkonganti@1 | 31 |
| kkonganti@1 | 32 export_plots: true |
| kkonganti@1 | 33 |
| kkonganti@1 | 34 # Run only these modules |
| kkonganti@1 | 35 run_modules: |
| kkonganti@1 | 36 - fastp |
| kkonganti@1 | 37 - fastqc |
| kkonganti@1 | 38 - custom_content |
| kkonganti@1 | 39 |
| kkonganti@1 | 40 module_order: |
| kkonganti@1 | 41 - fastp: |
| kkonganti@1 | 42 name: 'fastp' |
| kkonganti@1 | 43 info: > |
| kkonganti@1 | 44 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming |
| kkonganti@1 | 45 with <code>fastp</code> on SE, merged PE or concatenated PE reads. |
| kkonganti@1 | 46 path_filters: |
| kkonganti@1 | 47 - '*.fastp.json' |
| kkonganti@1 | 48 - fastqc: |
| kkonganti@1 | 49 name: 'FastQC' |
| kkonganti@1 | 50 info: > |
| kkonganti@1 | 51 section of the report shows FastQC results <b>before</b> adapter trimming |
| kkonganti@1 | 52 on SE, merged PE or concatenated PE reads. |
| kkonganti@1 | 53 path_filters: |
| kkonganti@1 | 54 - '*_fastqc.zip' |