Package: sequana-ribofinder
This is is theribofinderpipeline from theSequanaprojectOverview:Simple parallele workflow to detect and report ribosomal contentInput:FastQ filesOutput:HTML reportsStatus:productionCitation:Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352InstallationUsingpipfrom Python, just install this package:pip install sequana_ribofinder --upgradeThe–upgradeoption is to make sure you’ll get the latest version.UsageThis pipeline scans input fastq.gz files found in the local
directory and identify the proportion of ribosomal content.For help, please type:sequana_ribofinder --helpThe following command searches for input files in DATAPATH. Then, te user provide
a list of rRNA sequences in FastA format intest.fasta. This command creates a directory
called ribofinder/ where a snakemake pipeline can:sequana_ribofinder --input-directory DATAPATH --rRNA-file test.fastaYou will then need to execute the pipeline:cd ribofinder
sh ribofinder.sh  # for a local runThis launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:snakemake -s ribofinder.rules -c config.yaml --cores 4 --wrapper-prefix git+file:////home/user/sequana_wrappersOr usesequanixinterface.RequirementsThis pipelines requires the following executable(s):bowtie1 >= 1.3.0bedtoolssamtoolsbamtoolspigzDetailsThis pipeline runsribofinderin parallel on the input fastq files.
A brief sequana summary report is also produced.You can start from the reference file and the GFF file. By default we search for the feature called
rRNA to be found in the GFF file:sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gffIf the default feature rRNA is not found, no error is raised for now. If you know the expected feature,
you can provide it though:sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNAIf you have an existing or custom rRNA file, you can then use it as follows, in which case, no input reference is
required:sequana_ribofinder --input-directory . --rRNA-file ribo.fastaRules 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.ChangelogVersionDescription1.1.1hotfix for running on HPC (slurm)1.1.0Uses click (refactoring of sequana_pipetools)1.0.1add sequana_wrappers in the config/pipeline1.0.0use graphviz apptainer and latest wrappers0.13.0add  final apptainers and update CI actions0.12.0set singularity containers0.11.1Fix config file (removing hard-coded path)0.11.0Fix multiqc plot using same fix as in sequna_rnaseq pipelinesadd utility plot to check rate of  ribosomal per sequence and also
the corresponding  RPKM.0.10.2Fix the bowtie1 rule (all samples were named bowtie1)0.10.1add additional test and fix bug in pipeline (regression bug)0.10.0Update to use sequana-wrappers. Remove multiqc. summary.html
is self-content0.9.3fix logger0.9.2First release.