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comparison 0.5.0/conf/multiqc/nowayout_mqc.yml @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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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/sequoia/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 disable_version_detection: true
17 report_section_order:
18 kraken:
19 order: -994
20 NOWAYOUT_collated_table:
21 order: -995
22 NOWAYOUT_INDIV_READS_MAPPED_collated_table:
23 order: -996
24 fastp:
25 order: -997
26 fastqc:
27 order: -998
28 software_versions:
29 order: -999
30
31 export_plots: true
32
33 # Run only these modules
34 run_modules:
35 - fastqc
36 - fastp
37 - kraken
38 - custom_content
39
40 module_order:
41 - kraken:
42 name: "SOURMASH TAX METAGENOME"
43 href: "https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results"
44 doi: "10.21105/joss.00027"
45 info: >
46 section of the report shows how <b>reads</b> are approximately classified.
47 Please note that the plot title below is shown as
48 <b>Kraken2: Top taxa</b> since <code>kreport</code> fornat was used
49 to create Kraken-style reports with <code>sourmash tax metagenome</code>.
50 path_filters:
51 - "*.kreport.txt"
52 - fastqc:
53 name: "FastQC"
54 info: >
55 section of the report shows FastQC results <b>before</b> adapter trimming
56 on SE reads or on merged PE reads.
57 path_filters:
58 - "*_fastqc.zip"
59 - fastp:
60 name: "fastp"
61 info: >
62 section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
63 with <code>fastp</code> on SE reads or on merged PE reads.
64 path_filters:
65 - "*.fastp.json"