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comparison 0.5.0/conf/multiqc/bettercallsal_mqc.yml @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 title: CPIPES Report
2 intro_text: >
3 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2.
4 report_comment: >
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>
6 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
7 report_header_info:
8 - CPIPES Version: CPIPES_Version_Placeholder
9 - Workflow: Workflow_Name_Placeholder
10 - Workflow Version: Workflow_Version_Placeholder
11 - Conceived By: 'Kranti Konganti'
12 - Input Directory: Workflow_Input_Placeholder
13 - Output Directory: Workflow_Output_Placeholder
14 show_analysis_paths: False
15 show_analysis_time: False
16 report_section_order:
17 BETTERCALLSAL_SALMON_COUNTS:
18 order: -993
19 BETTERCALLSAL_SALYN_collated_table:
20 order: -994
21 BETTERCALLSAL_collated_table:
22 order: -995
23 BCS_SOURMASH_MATRIX_collated_table:
24 order: -996
25 fastp:
26 order: -997
27 fastqc:
28 order: -998
29 software_versions:
30 order: -999
31
32 export_plots: true
33
34 # Run only these modules
35 run_modules:
36 - fastp
37 - fastqc
38 - custom_content
39
40 module_order:
41 - fastp:
42 name: 'fastp'
43 info: >
44 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
45 with <code>fastp</code> on SE, merged PE or concatenated PE reads.
46 path_filters:
47 - '*.fastp.json'
48 - fastqc:
49 name: 'FastQC'
50 info: >
51 section of the report shows FastQC results <b>before</b> adapter trimming
52 on SE, merged PE or concatenated PE reads.
53 path_filters:
54 - '*_fastqc.zip'