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comparison 1.0.0/conf/multiqc/bettercallsal_lr_mqc.yml @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +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/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 skip_versions_section: True
17 disable_version_detection: true
18 report_section_order:
19 BETTERCALLSAL_SALMON_COUNTS:
20 order: -897
21 BETTERCALLSAL_SALYN_collated_table:
22 order: -898
23 BETTERCALLSAL_collated_table:
24 order: -899
25 BCS_SOURMASH_MATRIX_collated_table:
26 order: -900
27 MLST_collated_table:
28 order: -991
29 ABRICATE_NCBIAMRPLUS_collated_table:
30 order: -992
31 ABRICATE_MEGARES_collated_table:
32 order: -993
33 ABRICATE_RESFINDER_collated_table:
34 order: -994
35 ABRICATE_ARGANNOT_collated_table:
36 order: -995
37 filtlong:
38 order: -996
39 fastqc:
40 order: -997
41 fastqc-1:
42 order: -998
43 software_versions:
44 order: -999
45
46 export_plots: true
47
48 # Run only these modules
49 run_modules:
50 - filtlong
51 - fastqc
52 - custom_content
53
54 module_order:
55 - filtlong:
56 name: "filtlong"
57 info: >
58 section of the report shows read statistics <b>before</b> and <b>after</b> quality trimming
59 with <code>filtlong</code> on raw long reads.
60 path_filters:
61 - "*.filtlong.log"
62 - fastqc:
63 name: "FastQC (Raw reads)"
64 info: >
65 section of the report shows FastQC results <b>before</b> quality control
66 on long reads.
67 path_filters:
68 - "*.raw_fastqc.zip"
69 - fastqc:
70 name: "FastQC (Filtered reads)"
71 info: >
72 section of the report shows FastQC results <b>after</b> quality control
73 on long reads.
74 path_filters:
75 - "*.filtered_fastqc.zip"