Package: sequana-fastqc
This is is thefastqcpipeline from theSequanaprojetOverview:Runs fastqc and multiqc on a set of Sequencing data to produce control quality reportsInput:A set of FastQ files (paired or single-end) compressed or notOutput:An HTML file summary.html (individual fastqc reports, mutli-samples report)Status:ProductionWiki:https://github.com/sequana/fastqc/wikiDocumentation:This README file, the Wiki from the github repository (link above) andhttps://sequana.readthedocs.ioCitation:Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOIhttps://doi:10.21105/joss.00352Installationsequana_fastqc is based on Python3, just install the package as follows:pip install sequana_fastqc --upgradeYou will need third-party software such as fastqc. Please see below for details.UsageIf you have a set of FastQ files in a data/ directory, type:sequana_fastqc --input-directory dataTo know more about the options (e.g., add a different pattern to restrict the
execution to a subset of the input files, change the output/working directory,
etc):sequana_fastqc --helpThe call to sequana_fastqc creates a directoryfastqc. Then, you go to the
working directory and execute the pipeline as follows:cd fastqc
sh fastqc.sh  # for a local runThis launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters:snakemake -s fastqc.rules --cores 4 --stats stats.txtOr usesequanixinterface.Please see theWikifor more examples and features.TutorialYou can retrieve test data from sequana_fastqc (https://github.com/sequana/fastqc) or type:wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz
wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gzthen, prepare the pipeline:sequana_fastqc --input-directory .
cd fastqc
sh fastq.sh

# once done, remove temporary files (snakemake and others)
make cleanJust open the HTML entry called summary.html. A multiqc report is also available.
You will get expected images such as the following one:Please see theWikifor more examples and features.RequirementsThis pipelines requires the following executable(s):fastqcfalco (optional)For Linux users, we provide apptainer/singularity images available through thedamonaproject (https://damona.readthedocs.io).To make use of them, initiliase the pipeline with the –use-apptainer option and everything should be downloaded
automatically for you, which also guarantees reproducibility:sequana_fastqc --input-directory data --use-apptainer --apptainer-prefix ~/imagesDetailsThis pipeline runs fastqc in parallel on the input fastq files (paired or not)
and then execute multiqc. A brief sequana summary report is also produced.
s
You may use falco instead of fastqc. This is experimental but seem to work for
Illumina/FastQ files.This pipeline has been tested on several hundreds of MiSeq, NextSeq, MiniSeq,
ISeq100, Pacbio runs.It produces a md5sum of your data. It copes with empty samples. Produces
ready-to-use HTML reports, etcRules and configuration detailsHere is thelatest documented configuration fileto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.ChangelogVersionDescription1.8.2Fix the onerror typo in the pipeline, fix CI.1.8.1update __init__ (version)1.8.0uses pyproject instead of setuptoolsuses click instead of argparse and newest sequana_pipetools
(0.16.0)1.7.1Set wrapper version in the config based on new sequana_pipetools
feature1.7.0Use new rulegraph wrapper and new graphviz apptainer1.6.2slight refactorisation to use rulegraph wrapper1.6.1pin sequana version to 1.4.4 to force usage of new fastqc module
to fix falco. Updated config documentation.1.6.0Fixed falco output error and use singularity containers1.5.0removed modules completely.1.4.2simplified pipeline (suppress setup and use existing wrapper)1.4.1simplified pipeline with wrappers/rules1.4.0This version uses sequana 0.12.0 and new sequana-wrappers
mechanism. Functionalities is unchanged. Also based on
sequana_pipetools 0.6.X1.3.0add option –skip-multiqc (in case of memory trouble)Fix typo in the link towards fastqc reports in the summary.html
tableFix number of samples in the paired case (divide by 2)1.2.0compatibility with SequanixFix pipeline to cope with new snakemake API1.1.0add new rule to allow users to choose falco software instead of
fastqc. Note that fastqc is 4 times faster but still a work in
progress (version 0.1 as of Nov 2020).allows the pipeline to process pacbio files (in fact any files
accepted by fastqc i.e. SAM and BAM filesMore doc, test and info on the wiki1.0.1add md5sum of input files as md5.txt file1.0.0a stable version. Added a wiki on github as well and a
singularity recipes0.9.15For the HTML reports, takes into account samples with zero reads0.9.14round up some statistics in the main table0.9.13improve the summary HTML report0.9.12implemented new –from-project option0.9.11now depends on sequana_pipetools instead of sequana.pipelines to
speed up –help callsnew summary.html report created with pipeline summarynew rule (plotting)0.9.10simplify the onsuccess section0.9.9add missing png and pipeline (regression bug)0.9.8add missing multi_config file0.9.7check existence of input directory in main.pyadd a logofix schemaadd multiqc_configadd sequana + sequana_fastqc version0.9.6add the readtag optionContribute & Code of ConductTo contribute to this project, please take a look at theContributing Guidelinesfirst. Please note that this project is released with aCode of Conduct. By contributing to this project, you agree to abide by its terms.