pox-virus-tiled-amplicon-ref-masking 2.0
Visit source
Download RO-CrateFrom 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
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) |
|
| Reference FASTA | #main/Reference FASTA | The viral reference sequence to map sequenced reads against |
|
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 |
|
| masked_ref_pool2 | #main/masked_ref_pool2 | n/a |
|
Version History
2.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche
Added/updated 4 files
Open
master9617c19
Creators and Submitter
Views: 492 Downloads: 114
Created: 25th Jun 2024 at 10:54
Last updated: 25th Jun 2024 at 10:55
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
