pox-virus-tiled-amplicon-ref-masking
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/822?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 (earliest) Created 22nd Apr 2024 at 10:33 by Helena Rasche

Added/updated 3 files


Open master b8e5496
help Creators and Submitter
Creators
  • Viktoria Isabel Schwarz
  • Wolfgang Maier
Submitter
Tool
compute_sequence_length
License
MIT License
Activity

Views: 32

Created: 22nd Apr 2024 at 10:33

Last updated: 22nd Apr 2024 at 10:33

help Attributions

None

Total size: 33.2 KB
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