Workflows

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577 Workflows visible to you, out of a total of 682

Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs

Testing

Work-in-progress

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Type: COMPSs

Creator: Adam Hospital, Pau Andrio

Submitter: Stian Soiland-Reyes

Created: 29th Sep 2021 at 09:21

MaxQuant-RO-Crate

Testing

Work-in-progress

RO-Crate containing execution provenance about the MaxQuant-Workflow that analyze label-free data with MaxQuant based on Nextflow, running with SDRF implemented. Normalization and statistical comparisons using NormalyzerDE are conducted on the MaxQuant result

Type: Nextflow

Creator: Veit Schwämmle,Julian Uszkoreit

Submitter: Laura Rodriguez-Navas

Created: 8th Sep 2021 at 11:48, Last updated: 8th Sep 2021 at 15:42

sort-and-change-case-REUPLOAD

LifeMonitorDev

Tests Passing

sort lines and change text to upper case

Type: Galaxy

Creators: None

Submitter: Simone Leo

Created: 1st Sep 2021 at 13:22

sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING

LifeMonitorDev

Tests Not available

COVID-19: variation analysis reporting

This workflow takes table of variants produced by any of the other four variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates a list of variants by Samples and by Variant.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Simone Leo

Download

Created: 30th Aug 2021 at 17:00, Last updated: 30th Aug 2021 at 17:01

sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA

LifeMonitorDev

Tests Not available

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Simone Leo

Download

Created: 30th Aug 2021 at 17:00, Last updated: 30th Aug 2021 at 17:01

sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA

LifeMonitorDev

Tests Not available

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Simone Leo

Download

Created: 30th Aug 2021 at 17:00, Last updated: 30th Aug 2021 at 17:01

sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA

LifeMonitorDev

Tests Not available

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and, if possible, excludes reads derived from such ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Simone Leo

Download

Created: 30th Aug 2021 at 17:00, Last updated: 30th Aug 2021 at 17:00

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COVID-19: variation analysis reporting

COVID-19: variation analysis on WGS SE data

COVID-19: variation analysis on WGS PE data

COVID-19: variation analysis on ARTIC PE data

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