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comparison 0.2.0/conf/multiqc/cronology_mqc.yml @ 0:9e8b1c747a6a draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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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/cronology/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 MLST_collated_table:
18 order: -989
19 RMLST_collated_table:
20 order: -990
21 prokka:
22 order: -991
23 quast:
24 order: -992
25 ABRICATE_NCBIAMRPLUS_collated_table:
26 order: -993
27 ABRICATE_MEGARES_collated_table:
28 order: -994
29 ABRICATE_RESFINDER_collated_table:
30 order: -995
31 ABRICATE_ARGANNOT_collated_table:
32 order: -996
33 fastp:
34 order: -997
35 fastqc:
36 order: -998
37 software_versions:
38 order: -999
39
40 export_plots: true
41
42 # Run only these modules
43 run_modules:
44 - fastp
45 - fastqc
46 - prokka
47 - quast
48 - custom_content
49
50 module_order:
51 - fastp:
52 name: 'fastp'
53 info: >
54 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
55 with <code>fastp</code> on SE, merged PE or concatenated PE reads.
56 path_filters:
57 - '*.fastp.json'
58 - fastqc:
59 name: 'FastQC'
60 info: >
61 section of the report shows FastQC results <b>before</b> adapter trimming
62 on SE, merged PE or concatenated PE reads.
63 path_filters:
64 - '*_fastqc.zip'
65
66 # Custom module config
67 prokka_table: true
68