pox-virus-tiled-amplicon-ref-masking
2.0

Workflow Type: Galaxy

From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.

Associated Tutorial

This workflows is part of the tutorial pox-virus-tiled-amplicon-ref-masking, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Wolfgang Maier, Tomas Klingström

Workflow Author(s): Viktoria Isabel Schwarz, Wolfgang Maier

Funder(s): BeYond-COVID, ELIXIR-CONVERGE, Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe

SEEK ID: https://dev.workflowhub.eu/workflows/1078?version=1

Inputs

ID	Name	Description	Type
Primer Scheme	#main/Primer Scheme	The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)	File
Reference FASTA	#main/Reference FASTA	The viral reference sequence to map sequenced reads against	File

Steps

ID	Name	Description
2	Select pool1 primers	Grep1
3	Select pool2 primers	Grep1
4	Compute sequence length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3
5	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
6	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
7	Cut	Cut1
8	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
9	Get start position of Pool2	param_value_from_file
10	Get end position of sequence	param_value_from_file
11	Get end position of Pool1	param_value_from_file
12	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
13	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
14	Mask Reference for Pool2	toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0
15	Mask Reference for Pool1	toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0

Outputs

ID	Name	Description	Type
masked_ref_pool1	#main/masked_ref_pool1	n/a	File
masked_ref_pool2	#main/masked_ref_pool2	n/a	File

Version History

2.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche

Added/updated 4 files

Open master 9617c19

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tool

compute_sequence_length

License

MIT License

Activity

Views: 157 Downloads: 44

Created: 25th Jun 2024 at 10:54

Last updated: 25th Jun 2024 at 10:55

pox-virus-tiled-amplicon-ref-masking 2.0