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comparison 0.4.2/conf/multiqc/centriflaken_mqc.yml @ 0:082e0091e813 draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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1 title: CPIPES Report
2 intro_text: >
3 CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2.
4 report_comment: >
5 This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/centriflaken" 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 - Input Directory: Workflow_Input_Placeholder
12 - Output Directory: Workflow_Output_Placeholder
13 show_analysis_paths: False
14 show_analysis_time: False
15 report_section_order:
16 MLST_collated_table:
17 order: -989
18 ECTYPER_collated_table:
19 order: -990
20 SEROTYPEFINDER_collated_table:
21 order: -991
22 SEQSERO2_collated_table:
23 order: -992
24 ABRICATE_ECOLI_VF_collated_table:
25 order: -993
26 ABRICATE_NCBI_collated_table:
27 order: -994
28 ABRICATE_NCBIAMRPLUS_collated_table:
29 order: -995
30 ABRICATE_MEGARES_collated_table:
31 order: -996
32 ABRICATE_RESFINDER_collated_table:
33 order: -997
34 ABRICATE_ARGANNOT_collated_table:
35 order: -998
36 software_versions:
37 order: -999
38
39 export_plots: true
40
41 # Run only these modules
42 run_modules:
43 - fastqc
44 - kraken
45 - custom_content
46
47 module_order:
48 - fastqc:
49 name: "FastQC"
50 info: "section of the report shows FastQC results <b>before</b> adapter trimming."
51 path_filters:
52 - "*_fastqc.zip"
53 - kraken:
54 name: "Centrifuge"
55 href: "https://ccb.jhu.edu/software/centrifuge"
56 doi: "10.1101/gr.210641.116"
57 info: >
58 section of the report shows how <b>reads</b> are classified.
59 Please note that the plot title below is shown as
60 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
61 to create Kraken-style reports from centrifuge output files.
62 path_filters:
63 - "*.kreport.txt"
64 - kraken:
65 name: "Kraken2"
66 info: "section of the report shows how <b>assembled contigs</b> are classified."
67 path_filters:
68 - "*.report.txt"
69
70 extra_fn_clean_exts:
71 - ".centrifuge.kreport"
72 - ".report"
73
74 table_columns_visible:
75 Kraken: False
76 Kraken2: False
77 Centrifuge: False