Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/conf/multiqc/bettercallsal_mqc.yml @ 17:0e7a0053e4a6
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 title: CPIPES Report |
| kkonganti@17 | 2 intro_text: > |
| kkonganti@17 | 3 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. |
| kkonganti@17 | 4 report_comment: > |
| kkonganti@17 | 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@17 | 6 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory. |
| kkonganti@17 | 7 report_header_info: |
| kkonganti@17 | 8 - CPIPES Version: CPIPES_Version_Placeholder |
| kkonganti@17 | 9 - Workflow: Workflow_Name_Placeholder |
| kkonganti@17 | 10 - Workflow Version: Workflow_Version_Placeholder |
| kkonganti@17 | 11 - Conceived By: 'Kranti Konganti' |
| kkonganti@17 | 12 - Input Directory: Workflow_Input_Placeholder |
| kkonganti@17 | 13 - Output Directory: Workflow_Output_Placeholder |
| kkonganti@17 | 14 show_analysis_paths: False |
| kkonganti@17 | 15 show_analysis_time: False |
| kkonganti@17 | 16 report_section_order: |
| kkonganti@17 | 17 BETTERCALLSAL_SALMON_COUNTS: |
| kkonganti@17 | 18 order: -898 |
| kkonganti@17 | 19 BETTERCALLSAL_SALYN_collated_table: |
| kkonganti@17 | 20 order: -899 |
| kkonganti@17 | 21 BETTERCALLSAL_collated_table: |
| kkonganti@17 | 22 order: -900 |
| kkonganti@17 | 23 BCS_SOURMASH_MATRIX_collated_table: |
| kkonganti@17 | 24 order: -991 |
| kkonganti@17 | 25 MLST_collated_table: |
| kkonganti@17 | 26 order: -992 |
| kkonganti@17 | 27 ABRICATE_NCBIAMRPLUS_collated_table: |
| kkonganti@17 | 28 order: -993 |
| kkonganti@17 | 29 ABRICATE_MEGARES_collated_table: |
| kkonganti@17 | 30 order: -994 |
| kkonganti@17 | 31 ABRICATE_RESFINDER_collated_table: |
| kkonganti@17 | 32 order: -995 |
| kkonganti@17 | 33 ABRICATE_ARGANNOT_collated_table: |
| kkonganti@17 | 34 order: -996 |
| kkonganti@17 | 35 fastp: |
| kkonganti@17 | 36 order: -997 |
| kkonganti@17 | 37 fastqc: |
| kkonganti@17 | 38 order: -998 |
| kkonganti@17 | 39 software_versions: |
| kkonganti@17 | 40 order: -999 |
| kkonganti@17 | 41 |
| kkonganti@17 | 42 export_plots: true |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 # Run only these modules |
| kkonganti@17 | 45 run_modules: |
| kkonganti@17 | 46 - fastp |
| kkonganti@17 | 47 - fastqc |
| kkonganti@17 | 48 - custom_content |
| kkonganti@17 | 49 |
| kkonganti@17 | 50 module_order: |
| kkonganti@17 | 51 - fastp: |
| kkonganti@17 | 52 name: 'fastp' |
| kkonganti@17 | 53 info: > |
| kkonganti@17 | 54 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming |
| kkonganti@17 | 55 with <code>fastp</code> on SE, merged PE or concatenated PE reads. |
| kkonganti@17 | 56 path_filters: |
| kkonganti@17 | 57 - '*.fastp.json' |
| kkonganti@17 | 58 - fastqc: |
| kkonganti@17 | 59 name: 'FastQC' |
| kkonganti@17 | 60 info: > |
| kkonganti@17 | 61 section of the report shows FastQC results <b>before</b> adapter trimming |
| kkonganti@17 | 62 on SE, merged PE or concatenated PE reads. |
| kkonganti@17 | 63 path_filters: |
| kkonganti@17 | 64 - '*_fastqc.zip' |