Package: sequana-demultiplex
This is is thedemultiplexpipeline from theSequanaprojetOverview:Runs bcl2fastq on raw BCL data and creates plots to ease the QC validationInput:A valid Illumina base calling directory and sample sheet fileOutput:An HTML report, a set of PNG files and the expected FastQ filesStatus:productionWiki:https://github.com/sequana/demultiplex/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.00352InstallationIntall thesequana_demultiplexpackage as follows:pip install sequana_demultiplexUsagesequana_demultiplex --help
sequana_demultiplex --working-directory DATAPATH --bcl-directory bcldata --sample-sheet SampleSheet.csv --merging-strategy mergeThe –bcl-directory option indicates where to find your raw data, the sample-sheet
expects the SampleSheet to be compatible with IEM software. The –merging-strategy can
be set tononeormerge. Themergeoption merges the lanes, which is
useful for e.g. NextSeq sequencers.This creates a directoryfastq. You just need to execute the pipeline:cd demultiplex
sh demultiplex.sh  # for a local runThese commands launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the demultiplex.rules and config.yaml files and then execute the pipeline yourself with specific parameters:snakemake -s demultiplex.rules --cores 4 --stats stats.txt \
    --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/"You may also usesequanixfor a graphical interface.Would you need to merge the lane, please add the –merging-strategy argument
followed bymerge:sequana_demultiplex --bcl-directory bcl_data --merging-strategy merge --sample-sheet SampleSheet.csvRequirementsThis pipeline requires the following third-party tool(s):bcl2fastq 2.20.0This software has an end-user license agreement (EULA). Given the EULA details
of this software, it cannot be distributed according to ` Illumina license <https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-20-eula.pdf>`_
Therefore, you should install it yourself. On cluster facility, you may ask to
your system administator. For instance:module load bcl2fastq/2.20.0For the same reason you cannot find it on community such as bioconda or docker (aug 2020).So, you will need to download the code yourself. The easiest is to download the
RPM fromIlluminaand accept the agreements. Install it using the RPM if you have a debian-like system:rpm install file.rpmIf you do not have a debian system, you can look athttps://damona.readthedocs.iowhere we provide
a singularity recipes to build an image from your own  rpm. Recipes can be foundhere.DetailsThis pipeline runs bcl2fastq 2.20 and creates a set of diagnostics plots to help
deciphering common issues such as missing index and sample sheet errors.Rules 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.ChangelogVersionDescription1.5.2rename requirements.txt into tools.txt; update __init__1.5.1switch working directory to fastq instead of demultiplex(regression)1.5.0Uses click and new sequana_pipetools, add multiqc1.4.0Implement demultiplexing of single cell ATAC seq data with
cellranger.1.3.1use sequana_wrappers version in the config file1.3.0use latest sequana-wrappers to benefit and graphivz apptainer1.2.1Update CI action and use new sequana_pipetools v0.9.01.2.0stable release with cleanup of the setup and README1.1.3add the –mars-seq option that fills the config automatically1.1.2fix the none_and_force merging strategy option1.1.1fix a regression bug1.1.0Uses new sequana-wrappers repository1.0.5Fix regression bug to cope with new snakemake APICompatibility with sequanix GUI1.0.4Better HTML report with updated images.validate the SampleSheet when using sequana_demultiplex and/or the
pipelineAdd error handler from sequana_pipetoolssave all undetermined barcodes (not just first 20)No changes to the UItechnically, the input_directory option is now in a section so that
it can be used in Sequanix1.0.3remove check_samplesheet and fix_samplesheet modules now in sequanacheck sample sheet but do not fail. Instead, informing users that
there is an error and suggest to use ‘sequana samplesheet
–quick-fix’1.0.2Use ‘sequana samplesheet –check ‘ command instead of deprecated
sequana_check_sample_sheet command1.0.1change some default behaviour:write_fastq_reverse_complement is now set to False by default
like bcl2fastqThe –no-bgzf-compression option is changed into
–bgzf-compression. We do not want this option by default.The –ignore-missing-bcls option is changed into
–no-ignore-missing-bcls so as to ignore missing bcls by default
keep this option as a flag and keep same behaviourFix HTML syntax1.0.0stable version pinned on sequana libraries0.9.11fix label in plot_summary,add new plot to show reads per sample + undeterminedadd two tools one to check the samplesheet called
sequana_sample_sheet and one called sequana_fix_samplesheet. The
former is now inside the pipeline as well and when creating the
pipelineset –write_reverse_complement to False by defaultremove the –ignore-missing-control which is deprecated anyway0.9.10implement the new option –from-project, add missing MANIFEST0.9.9simplification of the pipeline to use sequana 0.8.4 to speed up
the –help calls.include a summary HTML report0.9.8fix typos0.9.7Use new release of sequana_pipetoolsset matplotlib backend to agginclude a simple HTML report0.9.6Handle different RunParameter.xml name (NextSeq vs HiSeq)0.9.5Fix a regression bug due to new sequana release. We do not check
the input file (fastq) since this is not a sequence analysis
pipelineCheck whether it is a NextSeq run. If so, merging-strategy must be
set to ‘merge’. Can be bypassed using –force0.9.4Check the presence of the bcl input directory and samplesheet.More help in the –help message.add  –sample-sheet option to replace –samplesheet optionFix the schema fileCheck for presence of RunParameters.xml and provide information
if merging-stratgy is set to None whereas it is a NextSeq run0.9.3Fix regression bug0.9.2remove warning due to relative paths.0.9.1Make the merging options compulsory. Users must tell whether they
want to merge the lanes or not. This avoid to do the merging or not
whereas the inverse was expected.0.8.6Uses 64G/biomics queue and 16 cores on a SLURM schedulerContribute & 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.