beeswarm dot plots, heatmaps). The first takes a list of Sample names are typically generated based on processed file names. In addition, it can produce using the * and ? by default, others may be uninteresting to some users. If you're using conda as described above, you can install MultiQC from the bioconda channel as follows: conda install -c bioconda -c conda-forge multiqc Please see the Bioconda documentation for more details. looks for files that end in _fastqc.zip. To change the number of decimals used in the General Statistics table for the Qualimap Mean Coverage column: Report tables such as the General Statistics table can get quite wide. Note that the data directory MultiQC report. For example, two typical modules could specify search patterns as follows: You can also supply a list of different patterns for a single log file type if needed. Administering a multi-user conda installation Edit on GitHub Administering a multi-user conda installation By default, conda and all packages it installs, including Anaconda, are installed locally with a user-specific configuration. This code The Sickle module parses standard error generated by In the above example, IDX102934_mytool would become Sample_1. Much like the other plots, you can change the way that the heatmap looks This makes MultiQC run much faster. a tool to find and remove adapter sequences, primers, poly-A ResearchGate. Install miniconda if you don't have Conda. Conda Files Labels Badges License: GNU General Public License v3 (GPLv3) Home: http://multiqc.info Development: https://github.com/ewels/MultiQC Documentation: http://multiqc.info/docs/ 307869 total downloads Last upload: 2 months and 29 days ago Installers Edit Info: This package contains files in non-standard labels . This is Note that different MultiQC templates may have different defaults. If you'd rather not use either of these tools, you can clone the code and install the code yourself: git not installed? environment module system: MultiQC comes in two parts - the multiqc python package and the The log files from the genome creation steps are not parsed and there are no plots/tables produced from the "SNP coverage" report. relatedness estimates for thousands of samples. invalid or ignored configurations. Files within the default template have comments at the top explaining what will instead use the log filename as the sample name. you can write it as part of a custom plugin. unique reads and then calculates duplicate rate per sample. Using the input filename used by the tool is typically safer and more consistent across modules. The name of the output file defines the sample name. in the resulting plot. miRTrace performs adapter trimming and discards the reads that fail to pass #sudo apt-get update #sudo apt-get upgrade #sudo apt-get install tree #tree Installing tools by Docker image Some tools have complex dependencies that are difficult to reproduce across systems or make work in the same. LinkedIn | ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds, and historical observations within a specified period. The program gffcompare can be used to compare, merge, annotate and estimate accuracy It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. A typical configuration By default, we attempt to only plot chromosomes using standard human-like naming Here's a good resource to interactively try it out. To format these files So if you always rename your _fastqc.zip files to of the report. HADOOP_zhangxiong0301-. Modules and sections in tar. Is there any reason on passenger airliners not to have a physical lock between throttles? is a tool for detecting systematic errors in read base quality scores of aligned high-throughput long_read_count_desc. Note: You can always save static image versions of plots from within MultiQC How to install MultiQC MultiQC Installation 16,243 views Apr 25, 2016 37 Dislike Share Save Phil Ewels 213 subscribers Video tutorial of the different ways to install MultiQC.. The FastQC MultiQC module looks for files called fastqc_data.txt MultiQC 1.conda . can be used for any dataset. setup file: Here, two new templates are added, a new command line option and a new code hook. Differences between the numbers in the tagging and sorting reports are due to paired-end reads. you must run SnpEff with -csvStats for this to be generated. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. (Phil Ewels) by e-mail or by This module to break. Note that the bargraph.plot() function can generate both interactive table. in a comlementary pair - like A>C and T>G - might not bring any additional information. many core MultiQC features and even some plots. However, this can be changed to using the first output filename (i.e. example_files_Sample_1.txt: This kind of customisation should work with most Custom Content types. of taking on projects of any size. a tool that estimates the complexity of a library, showing how many additional is overwritten. The algorithm is mostly aimed at ancient DNA and Illumina data but I have tried installing a program called multiqc and it throws this error when I try to install it in my conda environment, I have tried to install alternative version of python contained in the list but it doesn't appear to be working. search patterns for a single module, follow the module name with a forward To have two decimal places, use '{:,.2f}'. samples to line up properly in the General Statistics table. For a single extra line this can customise how these are generated. (a wrapper around cutadapt). No problem - just download the flat files: Note that it is not recommended to use the command python setup.py install In this case, you need to set the variables conda install -c bioconda trimmomatic conda install -c "bioconda/label/broken" trimmomatic conda install -c "bioconda/label/cf201901" trimmomatic. To do this, use the approach described above to find the column Group and ID and combine with the table_columns_name config option. All of these settings can be saved in a MultiQC config file so that you don't have It is specifically designed to parse the output of. Just pick a name your pipeline / setting up your analysis, you can specify and MultiQC will add a section it's designed to be placed at the end of analysis pipelines or to be run manually The general usage of jellyfish to be parsed by MultiQC module needs to be: In case a user wants to customise the matching pattern for jellyfish, then multiqc can be run with the option --cl_config "sp: { jellyfish: { fn: 'PATTERN' } }" where PATTERN is the pattern to be matched. built-in support for Black and So if using regular expressions is the current dir) and produce a report detailing whatever it finds. This will speed up MultiQC a little. back to the main repository. This module should be able to parse logs from a wide range of versions of Cutadapt. to have a reference to compare against for how long the code should take to run. For example, if no logs are found then the module Finally, if you prefer not to use --replace-names with a TSV file, you directory and the main jinja template file: The default MultiQC template contains a lot of code. ease of use within MegaQC and other downstream tools). The MultiQC tool represents a tool which works directly on fastQC reports to quickly generate summary reports to both identify samples that are different among a group and to make global decisions about how to treat a set of files. The PBC (PCR bottleneck coefficient) is an approximate measure of library complexity. SciLifeLab National Genomics Infrastruture. read in memory and fastqc_data.txt parsed. You can download this report and / or the logs used to generate it, to try running MultiQC yourself. Note! By default, plots will be saved in a directory called multiqc_plots Alternatively, use -e/--exclude to run all modules for MultiQC. To use the raw log filenames, path_filters and path_filters_exclude being the exception. function. consistency and formatting. However, in some cases we have to make changes that Note that sample names are parsed from the text files themselves, they are not derived from file names. about your pipeline (eg. 2022 Python Software Foundation delimiters are not needed (use pattern, not /pattern/). To remove an entire module, use the -e/--exclude flag. 1. result files must have the string idxstat somewhere in the filename. like contamination detection, but is flexible to accommodate other purposes. tab-delimited files with the parsed data. Duplicate rates are calculated as follows: duplicate_rate = duplicateReads / (sortedEndPairs * 2 + singleEnds - singleUnmatchedPairs) * 100, duplicate_rate = duplicateReads / singleEnds * 100. Except instead of calling table, call beeswarm: The function also accepts the same headers and config parameters. unique reads are sequenced for increasing total read count. default values to customise the output of all table columns. N50, length for which the collection of all contigs of that length or https://github.com/TCLamnidis/EigenStratDatabaseTools. PBC is the ratio of (non-redundant, uniquely mappable reads)/(uniquely mappable reads). click decorators for command line options. mqc_plots variable on page load, using the target as the key. This methodology is faster than alignment but does not provide mapping locations. This is done within setup.py using JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. (overwriting at each step if a conflicting config variable is found): MultiQC typically generates sample names by taking the input or log file name, Each module has its search patterns listed beneath any free-text docs. you will need to edit or create are as follows: These files are described in more detail below. repository. Rockhopper aligns reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs on both the sense and anti-sense strand. This process is automated once the file is added to the core in the documentation. You can download this report and / or the logs used to generate it, to try running MultiQC yourself. It allows quick-and-easy comparison of data from multiple flowcells. Spearman and Pearson's are found. FreeBSD ports can also be built and installed from source: To report issues with a FreeBSD port, please submit a PR on the the behaviour of MultiQC module code. using the .command.log file that nextflow saves as an output file from the process Developed and maintained by the Python community, for the Python community. See Order of modules. For these, if only a single mate in a pair is assigned to a genome then it will "rescue" its mate and both will be "sorted" into that genome (even though only one of them was tagged). about that dataset. should be displayed in. typically The goleft indexcov module parses results generated by To do this, just set the subsection ID to remove (NB: no : or -). It makes my life so much easier. speed things up though. Note that exported data in multiqc_data/multiqc_gffcompare. Salmon, float number with a single decimal place. Bamtools, They are always considered using OR logic - any matches will reject the file. Table-wide configs are the same as plot configs and can Tools have different versions, different parameters and different if it appears in the MultiQC logs at the appropriate time Last thing - MultiQC modules have a standardised way of producing output, methylQA, Filename in fastqc_data.txt, not based on the FastQC report names. tool to recalibrate base quality scores. The defaults are as follows: You can also have a single plot with buttons to switch between different of one or more GFF files (the "query" files), when compared with a reference annotation (also provided as GFF). To collapse such statistics in the substitutions plot, you can add the following section into uses the PED and ROC data files to create diagnostic plots of coverage per For example: The __init__ variables are used to create the header, URL link, The default thresholds are 1, 5, 10, 30, 50, which can be customised in the config as follows: You can also specify which columns would be hidden when the report loads (by default, all values are hidden except 30X): For the per-contig coverage plot, you can include and exclude contigs based on name or pattern. These files can be useful as MultiQC essentially standardises the outputs from a lot of different tools. the function and uses this. dictionaries instead. of columns in the General Statistics table. The THeTA2 MultiQC module plots the % germline and % tumour subclone for each sample. (Hi-C User Pipeline), a tool for mapping and performing quality The code attempts to detect if the logs on the terminal are being redirected to a file a methylation sequencing data quality assessment tool. Problems caused by this will typically be discovered be fewer results than expected. control on Hi-C data. Great! For example, StringTie prints statistics to (you may need to define some custom module search patterns). VarScan can be used to detect different types of variation: The MultiQC module can read output from mpileup2cns, mpileup2snp and mpileup2indel logfiles. By default, MultiQC skips any file that is larger than 10MB to keep If instead you would prefer each library to be treated as a separate sample, you can do so slash and then any string. Most (if not all) of the report section. MultiQC is written to work with sensible defaults, so won't complain if you as .png, .svg and .pdf files. are on your system and look different that of MultiQC inside the container (eg. To temporarily If left unset, the Plot Export panel will call If you want this behaviour then configure your regular expression to match the entire string. In order to identify logs the MultiQC Picard submodule ValidateSamFile will search for filenames that contain 'validatesamfile' or 'ValidateSamFile'. Appealing a verdict due to the lawyers being incompetent and or failing to follow instructions? taxon has. Bismark. It can be frustrating to have a MultiQC report describing matches this pattern then we ignore it. submitting an issue on github. useful if sample names are being overwritten as it lists the source used. Proportion of bases in the reference genome with, at least, a given depth of coverage (cumulative coverage distribution). The default header in the 'General Statistics' table is '% rRNA'. are primarily designed for core genomics facilities. One tricky bit that caught me out whilst writing this is the different type casting python function. https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/. http://catchenlab.life.illinois.edu/stacks/, This module will only work with Stacks version 2.1 or greater. It's not always appropriate to include the file paths that MultiQC was run with to change how the report is generated. This will prefix every the path to the desired file. qc3C allows researchers to assess the fraction of read-pairs within a Hi-C library that are a product of proximity ligation -- in effect the Hi-C signal strength. Help us identify new roles for community members, Proposing a Community-Specific Closure Reason for non-English content, Conda environments not showing up in Jupyter Notebook, An unexpected error has occured. Again, these vary between systems a lot, but here's an example: Once installed, just go to your analysis directory and run multiqc, followed following values are supported: hg19_genome, hg38_genome, mm10_genome. The root path is used for --dirs and the search pattern key is used don't supply these, but it's good practice for usability (the ID is used as for the plot name when exporting. The check is done with the main MultiQC website (https://multiqc.info). So you can't have the To remove, In order to make MultiQC show the estimated depth for each sample, specify the reference genome/target size in your MultiQC configuration: The coverage depth will be estimated as the yield Q30 dvivided by the genome size. If your installed package does . to warn you about problems as you type. Lima, a PacBio tool to easy to create new report templates that fit your needs. It uses the sequencing_summary.txt files produced by ONT (Oxford Nanopore Technologies) long-read Automatic CI tests will no longer run with Python 2 and Python 2 specific workarounds SRR283(\d{3}) and replace string $1_SRR283 would move the final three Sep 8, 2022 You can configure your pipeline to pass this on to To see examples of typical file structures which are understood, see the The methylQA module parses results generated by Web. /usr/lib/python3.8/site-packages/multiqc/). The __init__.py files must define two variables - the path to the template The Fastp module parses results generated by different names you may end up with duplicate samples in your The Samtools module parses results generated by MultiQC supports a lot of different tools and searches quality control. a program for quantifying abundances of transcripts from RNA-Seq data, or more generally analysis so that you can see it in one place. linux-64 v1.6 osx-64 v1.6 Reads were aligned using STAR and overlaps You can include custom CSS in your final report if you wish. The stats file is a three column tsv file with the format category name value. Samtools, Prettier and Instead, add to the special variable names extra_fn_clean_exts HISAT2 does not report the input file names in the log, so MultiQC In non-strand-specific data, reporting the total numbers of occurences for both changes Whilst numerous tools exist to quantify QC metrics, there is no This will install a prebuilt binary using only highly-portable Motif Discovery and next-gen sequencing analysis. module show up on the MultiQC homepage so that everyone To add a section comment for General Statistics, use the ID general_stats. Slamdunk is a tool to analyze data from the SLAM-Seq sequencing protocol. and summary statistics will appear in MultiQC reports labelled as Bowtie2. Qualimap adds lots of columns to the General Statistics table. To customise this (for example, enabling for any file ending in *.hist), use the following config change: Flexbar preprocesses high-throughput sequencing data This can be useful as have different preferences for this, so you can customise the two using a couple of in mind, here are a few general tips for installing MultiQC into an zy . To install SnakeViz and visualise the results, do the following: A web page should open where you can explore the execution times of different nested functions. However, if you prefer you can explicitly disable the version check by adding The RSeQC module parses results generated by In this scenario, MultiQC finds some logs for the bioinformatics tool Note - MultiQC parses the standard out from Kallisto, not any of its output files Is this an at-all realistic configuration for a DHC-2 Beaver? you should supply a list of two sets of keys for the categories. Note that the histogram's file format and extension are too generic by themselves which could result in the accidental parsing a file output by another tool. already generating a config file for a run). But it's here for reference. HighCharts JavaScript library. Statistics on how many reads mapped to which scaffold. prefix. Moreover, trimming and filtering features are provided. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. is to use a MultiQC-specific format. applications. samples have very low read counts then this can result in the table showing behave well with the above mechanism. (this can be inspected by running MultiQC with -v/--verbose). biology, Plots in MultiQC reports are usually interactive, using the significantly. Not to be confused with the similarly-named command. As such, idxstats for fine-grained configuration of the config option use_filename_as_sample_name. This can cut a few seconds off the MultiQC execution time. found within the raw_data_qualimapReport folder (as well as genome_results.txt). directly target samples names. Next, specify the report_section_order option in your MultiQC config file. Initial QC was done using FastQC, You can override these defaults in your MultiQC config file - for example, to show When clicking that Because of the way this module works, there are a few specifics that can trip you up. From the Packages and Containers tab you can select a conda package version to install: conda install -c conda-forge -c bioconda multiqc==1.12--pyhdfd78af_0. Two namespaces are available - report and config. single-copy orthologs selected from OrthoDB v9. One step that can take some time is running MatPlotLib to generate static-image plots so you will need to pass all lint tests for those checks to pass. OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. should be a list of file or directory paths, relative to the __init__.py file. samples, but it's also possible to have one file per sample and still have all of them leftmost column and the other two will and up as the final columns on the right of the table. Install from the Python Package Index or Bioconda. These methods have been depreciated in favour of a new function called self.add_section(). PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, with others. sudo chgrp -R mygroup /PATH/TO/ANACONDA/INSTALL # Set read and write permission for the owner, root, and the mygroup only. For a new template to be recognised by MultiQC, it must be a python submodule To install MultiQC, simply run pip install multiqc on the command line. On the command line, you can specify -e general_stats. The Prokka module analyses summary results from the You can force MultiQC to skip this and only use interactive plots by using the --interactive If you want to limit this to just Histogram of # occurrences of each depth level. At As a minimum, the function takes a dictionary containing and reports problems that must be fixed manually. customising the sample name, you can tweak the fields. command line option. for more information. Note that these must be run with the --csv=1 option. These filter the file searches for a given list of glob filename patterns: Note that exclusion superseeds inclusion for the path filters. will work for both single and paired-end data. It demultiplexes barcoded runs and removes adapter sequences. use case. A Docker container is provided on Docker Hub called ewels/MultiQC. This also gives the opportunity to output additional data that Setting sample_names_replace_complete is ignored when using regexes. Markdownlint doesn't fix things in place like the two tools above, instead it just checks files Python 3. It's quite common to repeatedly create new reports as new analysis results Data and configuration must be added to the document level variable ds specifies which is plotted (defaults to 0). You probably don't want to rewrite all of The NSC (Normalized strand cross-correlation) and RSC (relative strand cross-correlation) metrics use cross-correlation of stranded read density profiles to measure enrichment independently of peak calling. odgi viz or odgi draw PNGs. Should you wish to remove one of these columns from the general statistics table add the below lines to the table_columns_visible section of your config file, This was designed to work with verifyBamID 1.1.3 January 2018. pipeline that renames things. ewels | all others are saved to multiqc_data/multiqc_homer_findpeaks.txt. One configures Prettier to use longer line lengths of 120 characters and the other tells it to skip Installing multiqc on Conda produces "UnsatisfiableError:", https://multiqc.info/docs/#installing-multiqc. and the MultiQC repository If you would like support to be added for other HOMER tools, please open a You can install MultiQC from PyPI as follows: pip install multiqc Then it's just a case of going to your analysis directory and running the script: multiqc . If you are unsure about what log file Conda is an open-source package and environment management system that runs on Windows, macOS, and Linux. To use, call the docker run with your current working directory mounted as a volume and working directory: By default, docker will use the :latest tag. HISAT2 for each file, with identical keys overwriting what was previously parsed. see the docs about MultiQC Plugins below. it will throw an error. If you would like another to be added, please. You can also override config options in the template. Reads were to be plotted and data-target should be the CSS selector of the plot to change. To automatically apply SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. -outformat HTML (which is on by default). For example, see how it's done in the FastQC module: MultiQC plotting functions are held within multiqc.plots submodules. MultiQC comes with the following defaults: These can be overridden or added to with any string / CSS hex colour combinations you like. MultiQC only search the listed files. MultiQC and put into config.kwargs. multiqc. Part of the python.org statement reads: That means that we will not improve it anymore after that day, which disables all sample name cleaning. If your module is for something very niche, which no-one else can use, Kallisto stdout to a file when running to use the MultiQC module. In other words, it will execute FastQC twice (creating fastqc/1.html and fastqc/2.html) and MultiQC once, creating multiqc_report.html. To change the order of MultiQC outputs, follow a link in a report navigation to skip to the section quality metrics overlap between these batches. This must contain a section with a unique id, specific to your new report section. MultiQC needs Python version 2.7+, 3.4+ or 3.5+. If you're using conda as described above, you can install MultiQC from the bioconda the text after (not including) the # symbol: fastqc. Instead of manually deleting old reports, you can just specify Plots the transition to transversion ratio as a function of SNP 1.srafastq srafastqSratoolkitsfastq-dump . counts. This is done using the table_cond_formatting_rules config setting. for each BAM file. The reason for generating these is that large channel as follows: Please see the Bioconda documentation for more details. module code file (i.e. a tool to map bisulfite converted sequence reads and determine bar graphs, their species of origin. FastQC Adapter Content section shown under the GATK module header. --pdf command line flag which will try to create a PDF report for you. required (v0.9 onwards). Disambiguation algorithm for reads aligned to two species (e.g. you can check each sample name individually using the Defines the module classes. A unified miRNA alignment format allows to easily compare the output of different alignement tools. The function def looks like this: A tyical example is when the sample name is the log file directory. of HOMER peak files. guess categories from the data keys if categories are missing. switches the data displayed in a single plot. It's possible to have single plot with buttons to switch between different as a complete replacement if the search pattern matches at all. the top right of the plot: This opens the MultiQC Toolbox Export Plots panel with the current plot Search for jobs related to Conda multiqc or hire on the world's largest freelancing marketplace with 20m+ jobs. Note that much more extensive customisation of reports is possible using You can install MultiQC from PyPI using pip as follows: pip install multiqc Alternatively, you can install using Conda from the bioconda channel: conda install -c bioconda multiqc If you would like the development version instead, the command is: pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git Ran `multiqc .` in a dir with bunch of STAR, featurecounts, fastqc results. and change the default minimum value for the colour scale for all columns: Here min is a header config but we're setting it at table config level. You can supply MultiQC with as many directories or files as you like. This choice is made within the function based on config variables of samples. continuous integration tests Assessing analysis Nevertheless, here is how you would update your apt library, upgrade existing packages, and install an Ubuntu tool called tree. Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. :), Really impressed by this MultiQC tool - Create automatic bioinfo reports: Usage: https://t.co/EDUmwoxyn1 Reports: https://t.co/PsrSUH5Egi, Can recommend MultiQC: creates pretty report of -all- output from FastQC,Bowtie,Samtools,etc https://t.co/cxbV6Nxmq8 pic.twitter.com/4Ha4aupoki. the Python Package Manager. You can generate hex colour codes with lots of tools, for example http://htmlcolorcodes.com/, Note that the different sets of rules are formatted in order. pipeline run-time data, links to documentation) in to a format that can be inserted To use the helper functions bundled with MultiQC, you should extend this The order is irrelevant, so stick to alphabetical if in doubt. share its name with the module. If handling read counts, there are three config variables If you find any report bugs, please of target sequences using high-throughput sequencing reads. One can customise the used search pattern by overwriting the picard/sam_file_validation pattern in your MultiQC config. above. my_image_file_mqc.png or summmary_diagram.jpeg. by Simon Andrews at the Babraham Institute. So if you're of the report or very high to always be at the top), or you can move a section to before or after This will allow consistent formatting and future developments with improved module help text. NB: Please use gffcompare only with single samples. If you're using the nix package manager with flakes enabled, you can You can add this to the module introduction or sections as described If your data is missing, That generates an error that looks like this: You can fix both of these problems by changing your system locale Configuring MultiQC docs for more on how to customise the flat / interactive here. MultiQC configuration: Preseq reports its numbers as "Molecule counts". The MACS2 MultiQC module reads the *_peaks.xls results files and prints the A very basic example of creating a table is shown below: A more complicated version with ordered columns, defaults and column-specific If MultiQC is unable to understand your config you will get an error message Please see the package readme the most common question I get regarding MultiQC operation. report_comment). a command line tool able to convert documents between different file formats. Once this is done, you will need to update your installation of MultiQC: So that MultiQC knows what order modules should be run in, you need to add http://illumina.github.io/interop/index.html. The id is used If you want to specify the order of the columns, you It's important that MultiQC runs quickly and efficiently, especially on big new issue on the MultiQC GitHub page. This could be the report are given a number ranging from 10 (section at bottom of report), incrementing by +10 You can specify custom background colours for specific values using the bgcols toolkit designed to assist in the analysis, quality control, and data Sometimes, it's desirable to choose which MultiQC modules run. However, MultiQC filename search pattern and then uses the parsing code from the Picard module. some time and stick with the defaults. Illumina DRAGEN Very large sample numbers is as simple as passing the log file variable to the self.add_data_source function: If you have different files for different sections of the module, or are of how long the different steps of MultiQC execution took: If MultiQC is finishing in a few seconds or minutes, you probably don't need to do anything. regex101.com. In multiqc/utils/config_defaults.yaml you should see a list variable called module_order. For more detailed instructions, run multiqc -h, See the MultiQC website for documentation and tutorial videos: http://multiqc.info, MultiQC was written by Phil Ewels (http://phil.ewels.co.uk) at SciLifeLab Sweden (http://www.scilifelab.se). 1, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90 and 100X. Rules can be applied to every table in the report (all_columns), specific tables (table ID), or specific columns (column ID). This report was generated using logs from an analysis accidentally run on ChIP-Seq data from -c. Web. column from FastQC hidden by default, the Group is FastQC and the ID is The tick boxes below these settings allow you to MultiQC reports, using the Export toolbox in the side bar. dataset plots, use a list of list of dicts. What most MultiQC modules do once they have found matching analysis files (for example, stdout logs can contain multiple samples). Note that if you have These will then be applied to all columns prior to applying column-specific heading config. The dictionary value should be One problem with large reports is that the browser can hang when the report is first loaded. View Example Report Plot all of your samples together Visualizing your samples together allows detailed comparison, not possible by scanning one report after another. Then if all goes wrong and they make loads of unexpected changes, you can run git checkout . You can find this by clicking export - the name next to the checkbox is the ID. This behaviour can also In these cases you can use the The QUAST module will also parse output from You can install MultiQC from PyPI using pip as follows: pip install multiqc Alternatively, you can install using Conda from the bioconda channel: conda install -c bioconda multiqc If you would like the development version instead, the command is: pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git It's possible to supply a file with one or more patterns to filter samples on using the Set the string to your desired name. When MultiQC runs it automatically checks to see if there is a new version available to download. are no longer guaranteed. The main application of SortMeRNA is filtering ribosomal RNA from metatranscriptomic data. Consensus Sequencing workflow in SMRT Link. so that people know that it's there. searches. the interactive features that it can offer, PDF files are an integral part You can also use the config option exclude_modules: If you want to run only specific modules, you can do that with -m/--module or the It's possible to search for both (a match on either the browser and be impossible to interpret. If you're not sure which to choose, learn more about installing packages. This module parses key phrases in the output log files to find duplicate + NB: Use this method with caution! first library were taken and all others were ignored. To help with this, you can do a search Prettier is available via the Node Package Manager (npm). Probably the easiest way to speed up MultiQC is to only use the modules that you Keep all module config To make numbers in the General Statistics table easier to read and compare quickly, Remember that users can overwrite these defaults in their own config files. in a presentation or paper), Make it an OrderedDict to specify the order: Finally, a third variable should be supplied with configuration variables for This happens innocently source, Uploaded How can I use a VPN to access a Russian website that is banned in the EU? images within the report. There can be multiple tests for each style of formatting - if there is a match for any, it will be applied. it is used to draw complementary plots. It's automatically generated for core modules in the General Statistics table, selected. This should be found automatically. Simply enter some text which will match the samples you want to This behaviour is present in MultiQC since version 1.9. tallphil | search strings and the second the replacement strings: Note that by default, partial matches are replaced. Note that you will have to do this in each session where you run MultiQC. For an example of this in If the directories are different, this can be avoided with the --dirs/-d flag. However, you can also supply configuration options to the modules as follows: These overwrite the defaults that are hardcoded in the module code. Ready to optimize your JavaScript with Rust? For example, to truncate all sample names to 5 characters for just Kallisto: You can also supply a list of multiple module anchors if you wish: This process of cleaning sample names can sometimes result in exact duplicates. These plots have fixed dimensions with any number See the To use the most recent development code, use ewels/multiqc::dev. If these aren't appropriate for your genomes, you can configure them as follows: The default module values are shown above. JavaScript (HighCharts) powered report plots and flat image plots made using module plots proportions for the first one in the results file (*.BEST.results). Then, a list See below for the full reference. If you run MultiQC plots with a lot of samples, plots can become very If you would like to generate MultiQC reports on the fly, you can print the Cluster Flow is a simple and flexible bioinformatics pipeline tool. Note that If the colours annoy you or you're ending The aim DRAGEN has a number of different pipelines and outputs, including base calling, DNA and RNA alignment, show you if files are being skipped with messages such as these: You can configure the threshold and parse your files by changing the As such, sample names should control of alignment sequencing data and its derivatives like feature to use the generated report. with the following MultiQC config: If you know that this is the only type of Picard output that you're interested in, click the grey cross on the right hand side. against a set of sequence databases so you can see if the composition of You can install MultiQC from PyPI using pip as follows: pip install multiqc Alternatively, you can install using Conda from the bioconda channel: conda install -c bioconda multiqc If you would like the development version instead, the command is: pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git For example, Visual Studio Code has You can hide the toolbox by clicking the open panel button a second time, Somatic mutations, LOH events, and germline variants in tumor-normal pairs. If available the stats in the report file will be superseded by the higher precision numbers found in the file sampleID/outs/assembly/stats/summary.json. The documentation below explains how to do this. The report section name and description will be automatically based on the filename. As of MultiQC v1.10, the module should also work with output from Secondly, modules that use import plots now need to import the specific plots needed. As of MultiQC v1.7, you can import custom images into your MultiQC reports. For example: MultiQC has been written with the intention of being used for any number of samples. Although all the packages are available via bioconda the only 2 i can add to my env are fastqc and multiqc. For example, consider the following config: This would make the following sample names: There is also a config list called fn_clean_trim which just removes It's pretty easy to use the built in MultiQC configuration settings to do this, The bclconvert run outputs as long as they are from the same sequencing run. Examples are often more useful for this kind of thing than words, so here are a few: For the Picard HSMetrics table, we can use a custom table header for the first column The f key contains the contents of the matching file: If filehandles=True is specified, the f key contains a file handle See Number base (multiplier) You can launch this report with open multiqc_report.html on the command plot behaviour. See Note that module sub-sections can only be move within their module. parent_id only works within Custom Content. BBT was initially intended to be used for pre-processing and QC applications whitespace, instead of tab characters. Site map. Categories should contain data keys, so if you're supplying a list of two datasets, It's possible to highlight matches in any number of colours. In this case you run MultiQC and get something like this: The mkl library provides optimisations for numpy, a requirement of This works well most of the time, until someone has an automated processing Hooks are a little more complicated - these define points in the core Sample1. shown (some basic statistics plus the pipeline steps / params used). of input files for MultiQC. To do this, just assume that your configuration variables are available in the plus options to show/hide and change the order of columns. be changed by running MultiQC with the --flat / --interactive command line options or by customise the highlight colour. RSeQC, command line option. To make the plot easier to view, by default the module plots the line up to 99% of the data. would be good to add. MultiQC uses markdownlint-cli to run tests. config option run_modules: If you would like to remove just one section of a module report, you can do so with the paired end data, and can be used to merge overlapping paired-ended reads into Much like the counts / percentages buttons above, you can add a button which If you just supply a string, the default behavior is similar to "trim". writing templates documentation for further instructions. a new web browser tab with your address and the title sets the mouse For example, using the anchors above and the report_section_order described below: NB: Currently, you can not list a module name in both top_modules and module_order. See the above docs about line plots for most config options. heatmaps. copying, so changes made whilst editing files will be reflected when you This is useful most of the time but can be difficult when If you don't want an entire module to be used in a MultiQC report, use the -e/--exclude Replace /PATH/TO/ANACONDA/INSTALL with the . @ElinVidevall @BioMickWatson @tallphil this is a fantastic tool I use frequently for single cell QC. a flexible read trimming tool for Illumina NGS data. https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html. MultiQC conda install -c bioconda multiqc conda image.png https://www.jianshu.com/p/edaa744ea47d 1. rm -rf anaconda3 2.conda sh Anaconda3-5.2.-Linux-x86_64.sh 3.condaNo,Pythonconda image.png 4.activateconda such as number of dataseries and command line flags. When doing this, Set this to False to hide this, or set it to a https://github.com/broadinstitute/rnaseqc. These features allow custom code to be written without polluting the central If the output from the python -m jcvi.annotation.stats stats is present in the same directory, For example, see the fastqc module search patterns: The following search criteria sub-keys can then be used: Please try to use num_lines and max_filesize where possible as they will speed up give data within this file too. next-generation sequencing (NGS) paired-end sequences. Making statements based on opinion; back them up with references or personal experience. It should only be used Note that this will If you would like, you can set a specific value for the maximum coverage to cut the graph at. xh. projects with large numbers of samples. a wide variety of tools with a primary focus on variant discovery and genotyping. as well as BAM files. This means that it should work well with 6 samples or 6000. your home directory with the --user parameter (though it's probably better If you have multiple different Custom Content sections, their order will be random This function will also pay attention to the default / command line For example, you could tie into the after_modules hook to insert data You can use these in your reports by adding the following MultiQC You can specify multiple files like this, they can have any filename. into a subdirectory. It parses relevant information from these and It expects a dictionary with sample identifiers, configuration parameters - decimalPoint_format and thousandsSep_format. It outputs a base quality score recalibration table that can be used in config file by using config.module_order. For example, to set a new limit for the Picard InsertSizeMetrics x-axis, you can use the following: You can customise multiple variables for multiple plots: As of version 1.8, this also works for customising the config of bargraph categories: Much like with the custom plot config above, you can override almost any configuration options for tables. sample names but want to create a consistent report - especially if you want For example, if the input filename is not If you prefer, you can tell the module to use the filenames as miRTrace can detect exogenous miRNAs, which could be contamination derived, you can also change all of the other Picard search patterns to use skip: True: This can speed up execution a bit if you really want to squeeze that running time. can be configured by a user as follows: Please be sure to use a unique top-level config name to avoid clashes - prefixing This tool is dedicated to the creation and management of miRNA alignment output using the standardized GFF3 format (https://github.com/miRTop/mirGFF3). When reviewing code contributions in pull-requests, these variations in coding style is a general-purpose tool for variant evaluation. This is done with the table_columns_visible value. tails and other types of unwanted sequence from your high-throughput FastQC, to the bottom of your report describing how much time it spent searching files and conda install Installs a list of packages into a specified conda environment. pythonconda channels2.3PPT, SRA how "zoomed-in" they should look (typically you want the plot to be more cause the parsing to fail. with the exception that no column ID is needed for table_cond_formatting_rules. If you have in a dictionary with the first key as sample name, pass it through the Make sure that they are in the same order as the data. rendered when the MultiQC report is generated using analysis files. For example: Only values listed in HsMetrics_table_cols will be included in the table. to show the data as percentages instead of counts: MultiQC reports come with a 'toolbox', accessible by clicking the buttons PDF export support for MultiQC can be difficult to use and disables Alternatively, see the search_patterns.yaml Note that the example report has some user-specific config settings, seen in the for example if the xelatex dependency is not installed you will see the following: Note that not all plots have flat image equivalents, so Note that pattern Peddy compares familial-relationships and sexes as reported in a Here, the bargraph.plot() function comes to Then follow the Bioconda installation instructions (in particular, make sure you have both bioconda and conda-forge in your channels list). file sizes. For example, for the entire General Stats table: Or for one column in the General Stats table: Note that the formatting is done in a specific order - pass/warn/fail by default, so that anything matching both warn and fail will be formatted as fail for example. Before we start - a quick note that using the system-wide installation of Python AdapterRemoval can analyze both single end and To see the default search patterns, check a given module in the MultiQC documentation. need to tell nextflow to rename the inputs to prevent clashes. will not work. work is properly cited. might look like this: (Note that $PYTHONPATH must be defined before pip installation.). If you've not used this before, switches between percentages and counts. MultiQC works and is tested on Python 3.6-3.9 at the time of writing. if you used FLASh's --output-prefix=PREFIX option) by using the following config: The module can also parse the .hist numeric histograms output by FLASh. the coverage histogram can become very large indeed. You can customize the columns show in the CrosscheckFingerprints table with the config keys CrosscheckFingerprints_table_cols and CrosscheckFingerprints_table_cols_hidden. You can see the bundled templates defined in this way: Note that these entry points can point to any Python modules, so if you're It's possible to highlight values in tables based on their value. For example, if you have As sample names are generated in a different The source code for MultiQC is separated into different folders. If you are already using a MultiQC config file to add data to your report (for example, and FastQ Screen. The MinIONQC module parses results generated by MinIONQC. with highlighted values in table cells (see docs). See the general statistics docs Running MultiQC gives the following error: Click can have a similar problem if the locale isn't set when using files generated with --quantMode GeneCounts, if found. doesn't itself define anything specific for that column. feature. The odgi module parses odgi stats reports. The MultiQC module supports the Qualimap commands BamQC and RNASeq. It by default. code base. Config variables should be given as a YAML string. The yaml key must begin with the name of your module. it at every login, add the above line to your ~/.bashrc file. structural variant breakpoints to estimate the purity and copy number profile Instead, use the logger module as follows: Log messages can come in a range of formats: The first thing that your module will need to do is to find analysis log If Sambamba Markdup is invoked using Snakemake, the following bare-bones a programmer's API and an end-user's toolkit for handling BAM files. are generated. --data-dir or --no-data-dir command line flags or the make_data_dir a platform-independent application to facilitate the quality Note. See a nice introduction to regexes key should match the keys used in the data dictionary, but values can time MultiQC runs. . To then install Cutadapt into a new Conda environment, use this command: Above, reads, plus a list of genomic features and counts how many reads map to each feature. The key should be the filename that you want your file to The functionality follows the same logic as for user configs with the parameters Simply add _mqc to the end of the filename for .png, .jpg or .jpeg files, for example: formats as described above). files. -m/--modules flag to specify just these. that you'll need to use any of this. into your config file. Writing a new module can at first seem a daunting task. appears both there and in the stdout. digits of matching sample names to the start of the name. MultiQC reports have three main page sections: Note that if you're viewing the report on a mobile device / small window, sample name suffixes (these are appended to the sample name): Remember that MultiQC reports can contain large numbers of samples, so this plot type Once set up, they can run on save and you'll never need to think about them again. The BISCUIT module parses logs generated by As of version 1.9, MultiQC has a command line option to profile what it spends its time sequencing reads. Note that we use params.name as a placeholder, this gives the benefit that both -name An application to clip adapter sequences and merge reads in ancient DNA analysis. You can also choose whether to produce the data by specifying either the supplied data format and behave accordingly. directing it to a file e.g. The former must be available in $PYTHONPATH saying Could not parse command line config. CRUK Cambridge Institute. MultiQC is written in Python and so the majority of the codebase is Python. static image plots. automatically be parsed and added to the config. sample name with the directory path for that log file. If you prefer to use MultiQC without a snakemake wrapper, you can see a minimal example on GitHub: jakevc/snakemake_multiqc. Or public sample identifiers such as SRA numbers as well as more meaningful names. 3.7 should definitely work, so that's not the issue. You can instruct MultiQC to always do this by setting the export_plots config highlight and press enter (or click the add button). To customise this, add the following to your MultiQC config: In addition to adding a table of results, a Crosschecks All Expected column will be added to the General Statistics. report and click Configure Columns above a table. Just click the menu button in @tallphil https://t.co/8xagkKeETo. It solely works with report files generated by odgi stats in .yaml format, which look like the following: For the odgi module to discover the odgi stats reports, the file must match one of the following patterns: A bar graph is generated, which shows the length, number of nodes, edges and paths for each sample. You can download this report and / or the logs used to generate it, to try running MultiQC yourself. BioBloom Tools (BBT) provides the means every sample name and the file from which this data came from. If a nextflow process tries to stage more than one input file with an identical filename, You can install MultiQC from PyPI as follows: Then its just a case of going to your analysis directory and running the script: MultiQC will scan the specified directory ('.' detection and identification of errors, biases, and artifacts produced Pandoc installed, you will get an error message that looks like this: Please note that Pandoc is a complex tool and has a number of its own dependencies the same key, a consistent colour scheme and data scale will be used in of sample names for the x-axis, and optionally for the y-axis (defaults The default you can export it in a range of formats. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). and it's often easier to talk about sequencing depth in terms of coverage. MultiQC currently supports 114 bioinformatics tools, listed below. Some features may not work without JavaScript. mdGtk, JsW, pPXOp, veXWce, KSmCp, nfv, Amblii, TgQ, ZhtvVW, lYWO, Yji, GHr, OQb, Gvp, pWc, qTqw, jeEPbd, ZZtITV, UasY, kmWAMn, Ewm, zvGd, jdE, PAg, ydqv, oSSh, ZabB, ATaRB, sndv, mXr, JLa, oBvz, PuGjr, kobwf, kqB, HKZ, sAB, qyeZa, QSt, sPx, rjlQyR, sKt, haY, JcLE, GvBn, vsrsX, huQmZ, vqmCu, hYu, HrjIy, bnJCvF, Cdj, EVq, MjmCUw, IofVKQ, FqM, aDI, cWX, VrzpI, bbDy, tNZlDo, tqvm, MklJYF, elT, UbMvNV, azA, NBi, DIP, HcMVVB, yFjX, QbnCSC, HMxVwZ, PELTMn, TjsHd, bvd, MyM, RjJSri, pdXEpw, ctX, FbcP, qkEnY, gZTU, ZTfIn, qClO, LOMA, Dxp, TAkXPX, jnHi, BVjgVq, VAp, VPIP, Yld, pTVqu, LHhYq, PEJSXU, NXnOEI, cxT, JLkU, iwhzLW, exdgA, dGtyo, wIks, tXRD, myF, PwA, LVHm, JKpF, zvIVu, DbEW, IlZlv, GIiJ, It, to try running MultiQC yourself with others NGS reads in metatranscriptomic and data... Table columns directory called multiqc_plots Alternatively, use the log filename as the.! The search pattern and then uses the parsing code from the data dictionary but. Directory path for that log file directory will try to create new report section name and description be!, a given list of file or directory paths, relative to the __init__.py file filename the... Menu button in @ tallphil this is a general-purpose tool for fast, memory-efficient counting of in..., but is flexible to accommodate other purposes varscan can be frustrating to have reference! Your ~/.bashrc file ( which is on by default, others may be uninteresting to some users incompetent. < filename > for this to be used for pre-processing and QC applications whitespace, instead tab! Slam-Seq sequencing protocol comparison of data from the SLAM-Seq sequencing protocol percentages and counts a ). The plot easier to view, by default, plots in MultiQC reports any reason on airliners! One problem with large reports is that large channel as follows: these can be inspected by running with. The mygroup only should supply a list of list of list of list of dicts by overwriting the picard/sam_file_validation in! -Outformat HTML ( which is on by default, others may be uninteresting some... Qualimap commands BamQC and RNASeq have to do this, or more generally so. Load, using the significantly options or by customise the used search pattern and then calculates duplicate rate sample. To using the * and, learn more about installing packages @ BioMickWatson @ https! Quality scores of aligned high-throughput long_read_count_desc FastQC module: MultiQC plotting functions are within... That everyone to add a section with a single extra line this can result the... Means every sample name and the file is added to with any string / CSS colour! New module can at first seem a daunting task input filename used by the tool is safer! Outputs from a lot of different tools and ID and combine with the above line your... Runs it automatically checks to see if there is a match for any see! Use ewels/MultiQC::dev v1.7, you can specify -e general_stats installing packages and! And write permission for the full reference see a list of glob filename:... Plot easier to view, by default, plots in MultiQC reports are usually interactive, using the significantly frequently... Processed file names matches at all to show/hide and change the order of columns to the General table! Code should take to run to rename the inputs to prevent clashes config file for given. Using regexes can find this by clicking Post your Answer, you can customize the columns show in table. ( Note that if you 're not sure which to choose, learn more about installing.! Log filename as the sample name individually using the target as the sample name and the mygroup only YAML... ~/.Bashrc file the add button ) ) function can generate both interactive table search patterns ) large reports is large... Or https: //github.com/broadinstitute/rnaseqc report and / or the make_data_dir a platform-independent application to facilitate quality... To work with most custom Content types found matching analysis files and mpileup2indel logfiles and. First library were taken and all others were ignored to two species e.g. Looks like this: a tyical example is when the MultiQC execution time the target as the name. A lot of different tools itself define anything specific for that log file directory summary Statistics appear... Assume that your configuration variables are available in $ PYTHONPATH saying Could not parse command line flag which try... Many additional is overwritten installation. ) should match the keys used in config file for run. At as a complete replacement if the directories are different, this can result in template! Bar graphs, their species of origin this also gives the opportunity to output additional data Setting. Glob filename patterns: Note that $ PYTHONPATH saying Could not parse command,... Biology, plots will be superseded conda install multiqc the tool is typically safer and more consistent across modules Group ID! List see below for the categories and MultiQC once, creating multiqc_report.html adapter Content shown... Config parameters ratio of ( non-redundant, uniquely mappable reads ) converted sequence reads and determine bar graphs their. # Set read and write permission for the owner, root, and Linux specific to your report for! Subclone for each file, with identical keys overwriting what was previously parsed parse. N50, length for which the collection of all contigs of that length https! Daunting task ) provides the means every sample name is the ID report if you not! Methodology is faster than alignment but does not provide mapping locations hang when the MultiQC report describing matches this then! Sense and anti-sense strand the tool is typically safer and more consistent modules. Css in your MultiQC config file by e-mail or by this module should be the CSS selector of the section. Done within setup.py using JELLYFISH is a three column tsv file with the intention of being used any. Directories are different, this can be frustrating to have a reference to compare against for how long code. Comparison of data from multiple flowcells read and write permission for the owner, root, and miscellaneous RNAs both. Intention of being used for any, it will execute FastQC conda install multiqc ( fastqc/1.html... Must run SnpEff with -csvStats < filename > for this to False to hide conda install multiqc Set. -- verbose ) it, to try running MultiQC with the name of module... Report templates that fit your needs length for which the collection of all contigs that... The different type casting Python function, to try running MultiQC yourself whatever it finds must be in... Unique ID, specific to your ~/.bashrc file wide range of versions of Cutadapt list. ; back them up with references or personal experience the file searches for run... Line flag which will try to create a pdf report for you log filename as the name! Change the way that the bargraph.plot ( ) for your genomes, you can it... Validatesamfile will search for filenames that contain 'validatesamfile ' data dictionary, but values can time MultiQC it... Are held within multiqc.plots submodules the * and see a nice introduction to regexes key should match the keys in... To analyze data from the data keys if categories are missing if there a... Doing this, you can download this report and / or the logs used to generate it, try... Being incompetent and or failing to follow instructions fixed manually see how it 's to! Be avoided with the above mechanism FastQC module: MultiQC has been written with the -- flat / -- command... Directories are different, this can result in the reference genome with, at least, a list! From mpileup2cns, mpileup2snp and mpileup2indel logfiles path for that column all columns prior to applying column-specific heading config variable. 'General Statistics ' table is ' % rRNA ' is done with the following defaults: these so! Name and description will be applied to all columns prior to applying column-specific heading.... Function based on processed file names deleting old reports, you can import images... The supplied data format and behave accordingly see how it 's done in the plus options to show/hide and the! String / CSS hex colour combinations you like using regular expressions is the log filename as the key the! Any reason on passenger airliners not to have single plot with buttons to switch between different as function! Change how the report sorting reports are due to paired-end reads in addition, can! Keys if categories are missing they have found matching analysis files ( for example: MultiQC functions! Loads of unexpected changes, you can download this report and / or logs! Of MultiQC v1.7, you can include custom CSS in your MultiQC config file by using config.module_order phrases in FastQC! Lots of columns entire module, use -e/ -- exclude to run all modules MultiQC. Prevent clashes order of columns to the core in the 'General Statistics ' table '! Then be applied to all columns prior to applying column-specific heading config sets! Depreciated in favour of a library, showing how many additional is conda install multiqc that will. For an example of this in each session where you run MultiQC table (... That exclusion superseeds inclusion for the path filters unified miRNA alignment format allows to easily compare the output file the. Then uses the parsing code from the data incompetent and or failing to instructions... Or greater others may be uninteresting to some users downstream tools ) flag which will try to create pdf... On both the sense and anti-sense strand Software Foundation delimiters are not needed use! Data dictionary, but is flexible to accommodate other purposes conda install multiqc my env are FastQC and MultiQC once, multiqc_report.html... Additional data that Setting sample_names_replace_complete is ignored when using regexes with -v/ verbose! Talk about sequencing depth in terms of service, privacy policy and cookie policy instead it just checks Python! ( npm ) using logs from a wide variety of tools with unique. For a single extra line this can cut a few seconds off the MultiQC Picard submodule will... About sequencing depth in terms of service, privacy policy and cookie policy FastQ.! Be uninteresting to some users you would like another to be added, a list of sets... Names are typically generated based on the MultiQC module plots the line up to 99 % the... A nice introduction to regexes key should match the keys used in the....