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

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:

1. Year (ex: 2021)
2. month (ex: 1)
3. day (ex: 15)
4. Time (ex: 16:56)
5. Time zone (such as UTC)
6. 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

Non-functional workflow to get a global view of possibilities for plant virus classification.

Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.

Steps:

• SAPP: rdf2gtf (genome fasta)
• SAPP: rdf2fasta (transcripts fasta)
• STAR index (Optional for Eukaryotic origin)
• bowtie2 index
• kallisto index

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures