Workflows
What is a Workflow?Filters
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
Metagenomic dataset taxonomic classification using kraken2
Metagenomic dataset taxonomic classification using kraken2
Workflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- sam_to_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Amplicon analysis workflow using NG-Tax
Steps:
- Quality control on the reads
- Execute NGTax for ASV detection and classification
For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366
Type: Common Workflow Language
Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,
Submitter: Jasper Koehorst
This workflow is used to process timeseries from meteorological stations in Finland but can be applied to any timeseries according it follows the same format.
Take a temperature timeseries from any meteorological station. Input format is csv and it must be standardized with 6 columns:
- Year (ex: 2021)
- month (ex: 1)
- day (ex: 15)
- Time (ex: 16:56)
- Time zone (such as UTC)
- Air temperature (degC)
COnSensus Interaction Network InFErence Service
Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.
Reference
[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...
Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level
Workflow for tracking objects in Cell Profiler: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html