Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/conf/multiqc/cronology_mqc.yml @ 2:408603fd75ca
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 14:21:42 -0500 |
| parents | c8597e9e1a97 |
| 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/cronology/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 report_section_order: |
| kkonganti@0 | 17 MLST_collated_table: |
| kkonganti@0 | 18 order: -989 |
| kkonganti@0 | 19 RMLST_collated_table: |
| kkonganti@0 | 20 order: -990 |
| kkonganti@0 | 21 prokka: |
| kkonganti@0 | 22 order: -991 |
| kkonganti@0 | 23 quast: |
| kkonganti@0 | 24 order: -992 |
| kkonganti@0 | 25 ABRICATE_NCBIAMRPLUS_collated_table: |
| kkonganti@0 | 26 order: -993 |
| kkonganti@0 | 27 ABRICATE_MEGARES_collated_table: |
| kkonganti@0 | 28 order: -994 |
| kkonganti@0 | 29 ABRICATE_RESFINDER_collated_table: |
| kkonganti@0 | 30 order: -995 |
| kkonganti@0 | 31 ABRICATE_ARGANNOT_collated_table: |
| kkonganti@0 | 32 order: -996 |
| kkonganti@0 | 33 fastp: |
| kkonganti@0 | 34 order: -997 |
| kkonganti@0 | 35 fastqc: |
| kkonganti@0 | 36 order: -998 |
| kkonganti@0 | 37 software_versions: |
| kkonganti@0 | 38 order: -999 |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 export_plots: true |
| kkonganti@0 | 41 |
| kkonganti@0 | 42 # Run only these modules |
| kkonganti@0 | 43 run_modules: |
| kkonganti@0 | 44 - fastp |
| kkonganti@0 | 45 - fastqc |
| kkonganti@0 | 46 - prokka |
| kkonganti@0 | 47 - quast |
| kkonganti@0 | 48 - custom_content |
| kkonganti@0 | 49 |
| kkonganti@0 | 50 module_order: |
| kkonganti@0 | 51 - fastp: |
| kkonganti@0 | 52 name: 'fastp' |
| kkonganti@0 | 53 info: > |
| kkonganti@0 | 54 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming |
| kkonganti@0 | 55 with <code>fastp</code> on SE, merged PE or concatenated PE reads. |
| kkonganti@0 | 56 path_filters: |
| kkonganti@0 | 57 - '*.fastp.json' |
| kkonganti@0 | 58 - fastqc: |
| kkonganti@0 | 59 name: 'FastQC' |
| kkonganti@0 | 60 info: > |
| kkonganti@0 | 61 section of the report shows FastQC results <b>before</b> adapter trimming |
| kkonganti@0 | 62 on SE, merged PE or concatenated PE reads. |
| kkonganti@0 | 63 path_filters: |
| kkonganti@0 | 64 - '*_fastqc.zip' |
| kkonganti@0 | 65 |
| kkonganti@0 | 66 # Custom module config |
| kkonganti@0 | 67 prokka_table: true |
| kkonganti@0 | 68 |