This is the fastqc pipeline from the Sequana projet

Overview:	Runs fastqc (or falco) and multiqc on a set of sequencing data to produce quality control reports
Input:	A set of FastQ files (paired or single-end), compressed or not
Output:	An HTML summary report with individual FastQC reports and a multi-sample MultiQC report
Status:	Production
Documentation:	This README file 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

If you already have all requirements, you can install the package using pip:

pip install sequana_fastqc --upgrade

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

Usage

Scan FastQ files in a directory and set up the pipeline (replace DATAPATH with your input directory):

sequana_fastqc --input-directory DATAPATH

To use falco instead of fastqc:

sequana_fastqc --input-directory DATAPATH --method falco

To skip the MultiQC report (useful when memory is limited):

sequana_fastqc --input-directory DATAPATH --skip-multiqc

This creates a fastqc/ directory with the pipeline and configuration file. Execute the pipeline locally:

cd fastqc
sh fastqc.sh

If you are familiar with Snakemake, you can also run the pipeline directly:

snakemake -s fastqc.rules --cores 4 --stats stats.txt

See .sequana/profile/config.yaml to tune Snakemake behaviour (cores, cluster settings, etc.).

Usage with apptainer

With apptainer, initiate the working directory as follows:

sequana_fastqc --input-directory DATAPATH --use-apptainer

Images are downloaded in the working directory but you can store them in a shared location:

sequana_fastqc --input-directory DATAPATH --use-apptainer --apptainer-prefix ~/.sequana/apptainers

and then:

cd fastqc
sh fastqc.sh

Requirements

This pipeline requires the following executables (install via bioconda/conda):

• fastqc — quality control tool for sequencing data (default)
• falco — faster drop-in replacement for fastqc (optional, --method falco)
• multiqc — aggregated HTML report across samples

Install all dependencies at once:

mamba env create -f environment.yml

Details

This pipeline runs fastqc (or falco) in parallel on the input FastQ files, then aggregates results with MultiQC. A sequana summary report is also produced with per-sample statistics and quality plots.

QC method (--method):

• fastqc (default) — standard FastQC; handles FastQ, BAM, and SAM inputs
• falco — faster alternative; FastQ inputs only

Optional outputs:

• MultiQC report (multiqc/multiqc_report.html) — enabled by default, disable with --skip-multiqc
• MD5 checksums of all input files (md5.txt)
• Tree browser of individual FastQC HTML reports (tree.html)

This pipeline has been tested on several hundreds of MiSeq, NextSeq, MiniSeq, ISeq100, and PacBio runs.

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
1.10.0	Fix --skip-multiqc flag (was is_flag=False, now is_flag=True) Add multiqc_config rule so read_count_multiplier is written before multiqc runs (ordering fix) Restore config_file support in multiqc shell command Fix summary image link when multiqc is disabled Fix plotting_and_stats to use its own resources section Fix plotting_and_stats input (log files → declared outputs) Replace assert with raise ValueError in plotting_and_stats Use context manager for open() in onsuccess Extend localrules to dot2svg, md5sum, plotting_and_stats, multiqc_config Fix typo: detailled → detailed in HTML report Fix column label: duplicated (%) → unique (%) Remove stale sequana_wrappers version field from config.yaml Fix falco config comment (was copy-pasted from fastqc section) Remove redundant exclude_pattern assignment in main.py (SequanaManager handles it automatically)
1.9.0	Replace wrappers with shell commands via manager.get_shell() for falco, fastqc, multiqc, and dot2svg rules rulegraph rule uses manager.get_run() instead of wrapper
1.8.2	Fix the onerror typo in the pipeline, fix CI.
1.8.1	update __init__ (version)
1.8.0	uses pyproject instead of setuptools uses click instead of argparse and newest sequana_pipetools (0.16.0)
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.