|
kkonganti@0
|
1 custom_logo: "FDa-Logo-Blue---medium-01.png"
|
|
kkonganti@0
|
2 custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan"
|
|
kkonganti@0
|
3 custom_logo_title: "CFSAN, FDA"
|
|
kkonganti@0
|
4 title: CPIPES Report
|
|
kkonganti@0
|
5 intro_text: >
|
|
kkonganti@0
|
6 CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2.
|
|
kkonganti@0
|
7 report_comment: >
|
|
kkonganti@0
|
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>
|
|
kkonganti@0
|
9 analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
|
|
kkonganti@0
|
10 report_header_info:
|
|
kkonganti@0
|
11 - CPIPES Version: CPIPES_Version_Placeholder
|
|
kkonganti@0
|
12 - Workflow: Workflow_Name_Placeholder
|
|
kkonganti@0
|
13 - Workflow Version: Workflow_Version_Placeholder
|
|
kkonganti@0
|
14 - Input Directory: Workflow_Input_Placeholder
|
|
kkonganti@0
|
15 - Output Directory: Workflow_Output_Placeholder
|
|
kkonganti@0
|
16 - Developer E-mail: 'Kranti.Konganti@fda.hhs.gov'
|
|
kkonganti@0
|
17 - Stakeholder E-mail: 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
|
|
kkonganti@0
|
18 show_analysis_paths: False
|
|
kkonganti@0
|
19 show_analysis_time: False
|
|
kkonganti@0
|
20 report_section_order:
|
|
kkonganti@0
|
21 MLST_collated_table:
|
|
kkonganti@0
|
22 order: -989
|
|
kkonganti@0
|
23 ECTYPER_collated_table:
|
|
kkonganti@0
|
24 order: -990
|
|
kkonganti@0
|
25 SEROTYPEFINDER_collated_table:
|
|
kkonganti@0
|
26 order: -991
|
|
kkonganti@0
|
27 SEQSERO2_collated_table:
|
|
kkonganti@0
|
28 order: -992
|
|
kkonganti@0
|
29 ABRICATE_ECOLI_VF_collated_table:
|
|
kkonganti@0
|
30 order: -993
|
|
kkonganti@0
|
31 ABRICATE_NCBI_collated_table:
|
|
kkonganti@0
|
32 order: -994
|
|
kkonganti@0
|
33 ABRICATE_NCBIAMRPLUS_collated_table:
|
|
kkonganti@0
|
34 order: -995
|
|
kkonganti@0
|
35 ABRICATE_MEGARES_collated_table:
|
|
kkonganti@0
|
36 order: -996
|
|
kkonganti@0
|
37 ABRICATE_RESFINDER_collated_table:
|
|
kkonganti@0
|
38 order: -997
|
|
kkonganti@0
|
39 ABRICATE_ARGANNOT_collated_table:
|
|
kkonganti@0
|
40 order: -998
|
|
kkonganti@0
|
41 software_versions:
|
|
kkonganti@0
|
42 order: -999
|
|
kkonganti@0
|
43
|
|
kkonganti@0
|
44 export_plots: true
|
|
kkonganti@0
|
45
|
|
kkonganti@0
|
46 # Run only these modules
|
|
kkonganti@0
|
47 run_modules:
|
|
kkonganti@0
|
48 - fastqc
|
|
kkonganti@0
|
49 - kraken
|
|
kkonganti@0
|
50 - custom_content
|
|
kkonganti@0
|
51
|
|
kkonganti@0
|
52 module_order:
|
|
kkonganti@0
|
53 - fastqc:
|
|
kkonganti@0
|
54 name: 'FastQC'
|
|
kkonganti@0
|
55 info: 'section of the report shows FastQC results <b>before</b> adapter trimming.'
|
|
kkonganti@0
|
56 path_filters:
|
|
kkonganti@0
|
57 - '*_fastqc.zip'
|
|
kkonganti@0
|
58 - kraken:
|
|
kkonganti@0
|
59 name: 'Centrifuge'
|
|
kkonganti@0
|
60 href: 'https://ccb.jhu.edu/software/centrifuge'
|
|
kkonganti@0
|
61 doi: '10.1101/gr.210641.116'
|
|
kkonganti@0
|
62 info: >
|
|
kkonganti@0
|
63 section of the report shows how <b>reads</b> are classified.
|
|
kkonganti@0
|
64 Please note that the plot title below is shown as
|
|
kkonganti@0
|
65 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
|
|
kkonganti@0
|
66 to create Kraken-style reports from centrifuge output files.
|
|
kkonganti@0
|
67 path_filters:
|
|
kkonganti@0
|
68 - '*.kreport.txt'
|
|
kkonganti@0
|
69 - kraken:
|
|
kkonganti@0
|
70 name: 'Kraken2'
|
|
kkonganti@0
|
71 info: 'section of the report shows how <b>assembled contigs</b> are classified.'
|
|
kkonganti@0
|
72 path_filters:
|
|
kkonganti@0
|
73 - '*.report.txt'
|
|
kkonganti@0
|
74
|
|
kkonganti@0
|
75 extra_fn_clean_exts:
|
|
kkonganti@0
|
76 - '.centrifuge.kreport'
|
|
kkonganti@0
|
77 - '.report'
|
|
kkonganti@0
|
78
|
|
kkonganti@0
|
79 table_columns_visible:
|
|
kkonganti@0
|
80 Kraken: False
|
|
kkonganti@0
|
81 Kraken2: False
|
|
kkonganti@0
|
82 Centrifuge: False |
