MGnify's amplicon pipeline v5.0
1.0

Workflow Type: Galaxy

MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Workflow Author(s): EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep

Tutorial Author(s): Rand Zoabi

Tutorial Contributor(s): Paul Zierep, Saskia Hiltemann

Funder(s): German Competence Center Cloud Technologies for Data Management and Processing (de.KCD)

SEEK ID: https://workflowhub.eu/workflows/1853?version=1

ID	Name	Description
21	fastq-dl	toolshed.g2.bx.psu.edu/repos/iuc/fastq_dl/fastq_dl/3.0.1+galaxy0
22	Convert compressed file to uncompressed.	CONVERTER_gz_to_uncompressed
23	Convert compressed file to uncompressed.	CONVERTER_gz_to_uncompressed
24	Text reformatting	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
25	Text reformatting	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
26	Convert uncompressed file to compressed	CONVERTER_uncompressed_to_gz
27	Convert uncompressed file to compressed	CONVERTER_uncompressed_to_gz
28	MGnify's amplicon pipeline v5.0 - Quality control SE	n/a
29	MGnify's amplicon pipeline v5.0 - Quality control PE	n/a
30	Merge collections	__MERGE_COLLECTION__
31	MGnify's amplicon pipeline v5.0 - rRNA prediction	n/a
32	MGnify's amplicon pipeline v5.0 - ITS	n/a
33	Map empty/not empty collection to boolean	n/a
34	Map empty/not empty collection to boolean	n/a
35	Map empty/not empty collection to boolean	n/a
36	Map empty/not empty collection to boolean	n/a
37	MGnify amplicon summary tables	n/a
38	MGnify amplicon summary tables	n/a
39	ITSoneDB summary tables	n/a
40	UNITE summary tables	n/a

Added/updated 4 files

Open master 5bf775b

Creators and Submitter

Not specified

Discussion Channel

GTN Matrix

License

Activity

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Created: 11th Aug 2025 at 14:15