Abstract

This modified version of MultiQC added a module named NuGEN_dedup, which would process the data of deduplication by using NuGEN set for the extracellular RNA project.

Modified files:

setup.py (~/MultiQC/setup.py) add 'NuGEN_dedup = multiqc.modules.NuGEN_dedup:MultiqcModule' to the entry_points section

search_patterns.yaml (~/MultiQC/multiqc/utils/search_patterns.yaml) add search pattern to the search_patterns.yaml. The format of utput of NuGEN deduplication is *_dup_log.txt

NuGEN_dedup:
    fn: '*_dup_log.txt'

config_defaults.yaml (~/MultiQC/multiqc/utils/config_defaults.yaml) add the module to the top of module_order in config_defaults.yaml

module_order:
    # MultiQC general module for catching output from custom scripts
    - 'custom_content'
    - NuGEN_dedup:
        module_tag:
            - RNA

README.md (~/MultiQC/docs/README.md) add the information of added module NuGEN_dedup to the post-alignment section of README

Post-alignment:
    NuGEN_dedup: modules/NuGEN_dedup.md

Added directory and files

NuGEN_dedup.md (~docs/modules/NuGEN_dedup.md) added explianation file under the directory of doc. No meaningful content in this file

NuGEN_dedup (~/MultiQC/multiqc/modules/NuGEN_dedup) created directory under the directory of module. The name of directory should be the same as the name of module. This directory will hold the file of __init__.py and NuGEN_dedup.py.

NuGEN_dedup.py (~/MultiQC/multiqc/modules/NuGEN_dedup/NuGEN_dedup.py) The main program for add data to general stats and add section to the multiQC report. Name should be the same as the name of module

init.py (~/MultiQC/multiqc/modules/NuGEN_dedup/init.py) import all the modules that provided by MultiQC. Also creates the entry point for our module

Cuerrent MultiQC contains following tools.

[NuGEN_dedup]: [adapterremoval]: http://multiqc.info/docs/#adapter-removal [afterqc]: http://multiqc.info/docs/#afterqc [bamtools]: http://multiqc.info/docs/#bamtools [bbmap]: http://multiqc.info/docs/#bbmap [bcftools]: http://multiqc.info/docs/#bcftools [bcl2fastq]: http://multiqc.info/docs/#bcl2fastq [biobloomtools]: http://multiqc.info/docs/#biobloom-tools [bismark]: http://multiqc.info/docs/#bismark [bowtie-1]: http://multiqc.info/docs/#bowtie-1 [bowtie-2]: http://multiqc.info/docs/#bowtie-2 [busco]: http://multiqc.info/docs/#busco [clusterflow]: http://multiqc.info/docs/#cluster-flow [conpair]: http://multiqc.info/docs/#conpair [cutadapt]: http://multiqc.info/docs/#cutadapt [disambiguate]: http://multiqc.info/docs/#disambiguate [fastq-screen]: http://multiqc.info/docs/#fastq-screen [fastqc]: http://multiqc.info/docs/#fastqc [featurecounts]: http://multiqc.info/docs/#featurecounts [flexbar]: http://multiqc.info/docs/#flexbar [gatk]: http://multiqc.info/docs/#gatk [goleft]: http://multiqc.info/docs/#goleft-indexcov [hicexplorer]: http://multiqc.info/docs/#hicexplorer [hicup]: http://multiqc.info/docs/#hicup [hisat2]: http://multiqc.info/docs/#hisat2 [homer]: http://multiqc.info/docs/#homer [htseq]: http://multiqc.info/docs/#htseq [jellyfish]: http://multiqc.info/docs/#jellyfish [interop]: http://multiqc.info/docs/#interop [kallisto]: http://multiqc.info/docs/#kallisto [leehom]: http://multiqc.info/docs/#leehom [macs2]: http://multiqc.info/docs/#macs2 [methylqa]: http://multiqc.info/docs/#methylqa [peddy]: http://multiqc.info/docs/#peddy [picard]: http://multiqc.info/docs/#picard [preseq]: http://multiqc.info/docs/#preseq [prokka]: http://multiqc.info/docs/#prokka [qorts]: http://multiqc.info/docs/#qorts [qualimap]: http://multiqc.info/docs/#qualimap [quast]: http://multiqc.info/docs/#quast [rna_seqc]: http://multiqc.info/docs/#rna_seqc [rsem]: http://multiqc.info/docs/#rsem [rseqc]: http://multiqc.info/docs/#rseqc [salmon]: http://multiqc.info/docs/#salmon [samblaster]: http://multiqc.info/docs/#samblaster [samtools]: http://multiqc.info/docs/#samtools [sargasso]: http://multiqc.info/docs/#sargasso [skewer]: http://multiqc.info/docs/#skewer [slamdunk]: http://multiqc.info/docs/#slamdunk [snpeff]: http://multiqc.info/docs/#snpeff [sortmerna]: http://multiqc.info/docs/#sortmerna [star]: http://multiqc.info/docs/#star [supernova]: http://multiqc.info/docs/#supernova [theta2]: http://multiqc.info/docs/#theta2 [tophat]: http://multiqc.info/docs/#tophat [trimmomatic]: http://multiqc.info/docs/#trimmomatic [vcftools]: http://multiqc.info/docs/#vcftools [verifyBAMID]: http://multiqc.info/docs/#verifybamid