Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:801b85b03a17
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 report_section_order:
18 BETTERCALLSAL_SALMON_COUNTS:
19 order: -898
20 BETTERCALLSAL_SALYN_collated_table:
21 order: -899
22 BETTERCALLSAL_collated_table:
23 order: -900
24 BCS_SOURMASH_MATRIX_collated_table:
25 order: -991
26 MLST_collated_table:
27 order: -992
28 ABRICATE_NCBIAMRPLUS_collated_table:
29 order: -993
30 ABRICATE_MEGARES_collated_table:
31 order: -994
32 ABRICATE_RESFINDER_collated_table:
33 order: -995
34 ABRICATE_ARGANNOT_collated_table:
35 order: -996
36 fastp:
37 order: -997
38 fastqc:
39 order: -998
40 software_versions:
41 order: -999
42
43 export_plots: true
44
45 # Run only these modules
46 run_modules:
47 - fastp
48 - fastqc
49 - custom_content
50
51 module_order:
52 - fastp:
53 name: "fastp"
54 info: >
55 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
56 with <code>fastp</code> on SE, merged PE or concatenated PE reads.
57 path_filters:
58 - "*.fastp.json"
59 - fastqc:
60 name: "FastQC"
61 info: >
62 section of the report shows FastQC results <b>before</b> adapter trimming
63 on SE, merged PE or concatenated PE reads.
64 path_filters:
65 - "*_fastqc.zip"