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comparison 0.4.2/conf/multiqc/centriflaken_hy_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 custom_logo: "FDa-Logo-Blue---medium-01.png"
2 custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan"
3 custom_logo_title: "CFSAN, FDA"
4 title: CPIPES Report
5 intro_text: >
6 CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2.
7 report_comment: >
8 This report has been generated by the <a href="https://cfsan-git.fda.gov/Kranti.Konganti/cpipes/blob/master/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
9 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
10 report_header_info:
11 - CPIPES Version: CPIPES_Version_Placeholder
12 - Workflow: Workflow_Name_Placeholder
13 - Workflow Version: Workflow_Version_Placeholder
14 - Input Directory: Workflow_Input_Placeholder
15 - Output Directory: Workflow_Output_Placeholder
16 - Developer E-mail: "Kranti.Konganti@fda.hhs.gov"
17 - Stakeholder E-mail: "Narjol.Gonzalez-Escalona@fda.hhs.gov"
18 show_analysis_paths: False
19 show_analysis_time: False
20 report_section_order:
21 MLST_collated_table:
22 order: -989
23 ECTYPER_collated_table:
24 order: -990
25 SEROTYPEFINDER_collated_table:
26 order: -991
27 SEQSERO2_collated_table:
28 order: -992
29 ABRICATE_ECOLI_VF_collated_table:
30 order: -993
31 ABRICATE_NCBI_collated_table:
32 order: -994
33 ABRICATE_NCBIAMRPLUS_collated_table:
34 order: -995
35 ABRICATE_MEGARES_collated_table:
36 order: -996
37 ABRICATE_RESFINDER_collated_table:
38 order: -997
39 ABRICATE_ARGANNOT_collated_table:
40 order: -998
41 software_versions:
42 order: -999
43
44 export_plots: true
45
46 # Run only these modules
47 run_modules:
48 - fastqc
49 - kraken
50 - custom_content
51
52 module_order:
53 - fastqc:
54 name: "FastQC"
55 info: "section of the report shows FastQC results <b>before</b> adapter trimming."
56 path_filters:
57 - "*_fastqc.zip"
58 - kraken:
59 name: "Centrifuge"
60 href: "https://ccb.jhu.edu/software/centrifuge"
61 doi: "10.1101/gr.210641.116"
62 info: >
63 section of the report shows how <b>reads</b> are classified.
64 Please note that the plot title below is shown as
65 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
66 to create Kraken-style reports from centrifuge output files.
67 path_filters:
68 - "*.kreport.txt"
69 - kraken:
70 name: "Kraken2"
71 info: "section of the report shows how <b>assembled contigs</b> are classified."
72 path_filters:
73 - "*.report.txt"
74
75 extra_fn_clean_exts:
76 - ".centrifuge.kreport"
77 - ".report"
78
79 table_columns_visible:
80 Kraken: False
81 Kraken2: False
82 Centrifuge: False