Assembly-decontamination-VGP9/main
v0.1.4 (latest)

v0.1.4 (latest)

v0.1.3

v0.1.2

v0.1.1

v0.1 (earliest)

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Run on usegalaxy.eu

Workflow Type: Galaxy

Tests Passing

No description specified

SEEK ID: https://workflowhub.eu/workflows/645?version=5

Inputs

ID	Name	Description	Type
Database for Kraken2	Database for Kraken2	Select the database to query to identify non-target contaminants.	string
Scaffolded assembly (fasta)	Scaffolded assembly (fasta)	n/a	File

Steps

ID	Name	Description
2	lower to uppercase	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
3	soft-masking	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1
4	hard-masking	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
5	ID non-target contaminants	toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
6	blast mitochondria DB	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1
7	contaminant scaffolds	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
8	parsing blast output	toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0
9	remove > + lowercase	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
10	to lowercase	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
11	isolate scaffolds names	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
12	concatenate scaffold lists	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
13	removing scaffolds	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0

Outputs

ID	Name	Description	Type
Kraken2 classification scores	Kraken2 classification scores	n/a	File
full contaminant + mito scaffold list	full contaminant + mito scaffold list	n/a	File
final decontaminated assembly	final decontaminated assembly	n/a	File

Version History

v0.1.4 (latest) Created 14th Mar 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1.4

Frozen v0.1.4 e46571e

v0.1.3 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.3

Frozen v0.1.3 71692ba

v0.1.2 Created 21st Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.2

Frozen v0.1.2 b1c8ba6

v0.1.1 Created 14th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.1

Frozen v0.1.1 867840b

v0.1 (earliest) Created 8th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 f74cf72

Creators and Submitter

Creators

Not specified

Additional credit

Nadolina Brajuka

Submitter

WorkflowHub Bot

License

BSD 3-Clause "New" or "Revised" License (BSD-3-Clause)

Activity

Views: 1604

Created: 8th Nov 2023 at 03:01

Last updated: 14th Mar 2024 at 03:01

Assembly-decontamination-VGP9/main v0.1.4 (latest) v0.1.4 (latest) v0.1.3 v0.1.2 v0.1.1 v0.1 (earliest)