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A fastqc pipeline from sequana project.

Project description

https://badge.fury.io/py/sequana-fastqc.svg JOSS (journal of open source software) DOI https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg

This is is the fastqc pipeline from the Sequana projet

Overview:

Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports

Input:

A set of FastQ files (paired or single-end) compressed or not

Output:

an HTML file summary.html (individual fastqc reports, mutli-samples report)

Status:

production

Wiki:

https://github.com/sequana/fastqc/wiki

Documentation:

This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io

Citation:

Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352

Installation

sequana_fastqc is based on Python3, just install the package as follows:

pip install sequana_fastqc --upgrade

You will need third-party software such as fastqc. Please see below for details.

Usage

This command will scan all files ending in .fastq.gz found in the local directory, create a directory called fastqc/ where a snakemake pipeline is launched automatically. Depending on the number of files and their sizes, the process may be long:

sequana_fastqc --run

To 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 --help
sequana_fastqc --input-directory DATAPATH

This creates a directory fastqc. You just need to execute the pipeline:

cd fastqc
sh fastqc.sh  # for a local run

This 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.txt

Or use sequanix interface.

Please see the Wiki for more examples and features.

Tutorial

You 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.gz

then, prepare the pipeline:

sequana_fastqc --input-directory .
cd fastqc
sh fastq.sh

# once done, remove temporary files (snakemake and others)
make clean

Just open the HTML entry called summary.html. A multiqc report is also available. You will get expected images such as the following one:

https://github.com/sequana/fastqc/blob/main/doc/summary.png?raw=true

Please see the Wiki for more examples and features.

Requirements

This pipelines requires the following executable(s):

  • fastqc

  • falco (optional)

For Linux users, we provide singularity images available through within the damona project (https://damona.readthedocs.io).

To mak use of them, initiliase the pipeline with the –use-singularity option and everything should be downloaded automatically for you, which also guarantees reproducibility:

sequana_fastqc --input-directory data --use-singularity
https://raw.githubusercontent.com/sequana/fastqc/main/sequana_pipelines/fastqc/dag.png

Details

This 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, etc

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Version

Description

1.7.1

  • Set wrapper version in the config based on new sequana_pipetools feature

1.7.0

  • Use new rulegraph wrapper and new graphviz apptainer

1.6.2

  • slight refactorisation to use rulegraph wrapper

1.6.1

  • pin sequana version to 1.4.4 to force usage of new fastqc module to fix falco. Updated config documentation.

1.6.0

  • Fixed falco output error and use singularity containers

1.5.0

  • removed modules completely.

1.4.2

  • simplified pipeline (suppress setup and use existing wrapper)

1.4.1

  • simplified pipeline with wrappers/rules

1.4.0

  • This version uses sequana 0.12.0 and new sequana-wrappers mechanism. Functionalities is unchanged. Also based on sequana_pipetools 0.6.X

1.3.0

  • add option –skip-multiqc (in case of memory trouble)

  • Fix typo in the link towards fastqc reports in the summary.html table

  • Fix number of samples in the paired case (divide by 2)

1.2.0

  • compatibility with Sequanix

  • Fix pipeline to cope with new snakemake API

1.1.0

  • add 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 files

  • More doc, test and info on the wiki

1.0.1

  • add md5sum of input files as md5.txt file

1.0.0

  • a stable version. Added a wiki on github as well and a singularity recipes

0.9.15

  • For the HTML reports, takes into account samples with zero reads

0.9.14

  • round up some statistics in the main table

0.9.13

  • improve the summary HTML report

0.9.12

  • implemented new –from-project option

0.9.11

  • now depends on sequana_pipetools instead of sequana.pipelines to speed up –help calls

  • new summary.html report created with pipeline summary

  • new rule (plotting)

0.9.10

  • simplify the onsuccess section

0.9.9

  • add missing png and pipeline (regression bug)

0.9.8

  • add missing multi_config file

0.9.7

  • check existence of input directory in main.py

  • add a logo

  • fix schema

  • add multiqc_config

  • add sequana + sequana_fastqc version

0.9.6

add the readtag option

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

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