mgnify-amplicon-pipeline-v5-complete/main
v0.1 (earliest)

v0.2 (latest)

v0.1 (earliest)

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Workflow Type: Galaxy

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

SEEK ID: https://workflowhub.eu/workflows/1274?version=1

Inputs

Steps

ID	Name	Description
21	fastq-dl	toolshed.g2.bx.psu.edu/repos/iuc/fastq_dl/fastq_dl/3.0.0+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/9.3+galaxy1
25	Text reformatting	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
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

Outputs

Version History

v0.2 (latest) Created 26th Mar 2025 at 09:52 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 731cdfa

v0.1 (earliest) Created 4th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 bf4348a

Creators and Submitter

Creators

Rand Zoabi
Paul Zierep

Additional credit

EMBL's European Bioinformatics Institute

Submitter

WorkflowHub Bot

License

Apache License 2.0 (Apache-2.0)

Activity

Views: 2467 Downloads: 2732 Runs: 2

Created: 4th Feb 2025 at 03:02

ID	Name	Description	Type
Ambiguity filtering maximal N percentage threshold to conserve sequences	Ambiguity filtering maximal N percentage threshold to conserve sequences	Maximal N percentage threshold to conserve sequences.	int?
Clan information file	Clan information file	Clan information file.	File
ITS UNITE DB phylum level taxonomic abundance summary table name	ITS UNITE DB phylum level taxonomic abundance summary table name	n/a	string?
ITS UNITE DB taxonomic abundance summary table name	ITS UNITE DB taxonomic abundance summary table name	n/a	string?
ITSoneDB phylum level taxonomic abundance summary table name	ITSoneDB phylum level taxonomic abundance summary table name	n/a	string?
ITSoneDB taxonomic abundance summary table name	ITSoneDB taxonomic abundance summary table name	n/a	string?
LSU phylum level taxonomic abundance summary table name	LSU phylum level taxonomic abundance summary table name	n/a	string?
LSU taxonomic abundance summary table name	LSU taxonomic abundance summary table name	n/a	string?
Length filtering minimum size	Length filtering minimum size	Minimum sequence length.	int?
PE fastp - Enable base correction	PE fastp - Enable base correction	Enable base correction in overlapped regions. (Paired-end)	boolean?
PE fastp - Length required	PE fastp - Length required	Reads shorter than this value will be discarded. (Paired-end)	int?
PE fastp - Qualified quality phred	PE fastp - Qualified quality phred	The quality value that a base is qualified. (Paired-end)	int?
PE fastp - Unqualified percent limit	PE fastp - Unqualified percent limit	How many percents of bases are allowed to be unqualified (0~100). (Paired-end)	int?
SRA accession list	SRA accession list	List of SRA accession IDs, one per line.	File
SSU phylum level taxonomic abundance summary table name	SSU phylum level taxonomic abundance summary table name	n/a	string?
SSU taxonomic abundance summary table name	SSU taxonomic abundance summary table name	n/a	string?
Trimmomatic leading	Trimmomatic leading	Cut bases off the start of a read, if below a threshold quality.	int?
Trimmomatic min length	Trimmomatic min length	Minimum length of reads to be kept.	int?
Trimmomatic sliding window average quality	Trimmomatic sliding window average quality	Average quality required.	int?
Trimmomatic sliding window number of bases to average across	Trimmomatic sliding window number of bases to average across	Number of bases to average across.	int?
Trimmomatic trailing	Trimmomatic trailing	Cut bases off the end of a read, if below a threshold quality.	int?

ID	Name	Description	Type
Single-end post quality control FASTA files	Single-end post quality control FASTA files	n/a	File
Single-end MultiQC statistics	Single-end MultiQC statistics	n/a	File
Single-end MultiQC report	Single-end MultiQC report	n/a	File
Paired-end MultiQC report	Paired-end MultiQC report	n/a	File
Paired-end MultiQC statistics	Paired-end MultiQC statistics	n/a	File
Paired-end post quality control FASTA files	Paired-end post quality control FASTA files	n/a	File
LSU and SSU BED regions	LSU and SSU BED regions	n/a	File
LSU OTU tables (SILVA DB)	LSU OTU tables (SILVA DB)	n/a	File
SSU taxonomic classifications using SILVA DB	SSU taxonomic classifications using SILVA DB	n/a	File
SSU FASTA files	SSU FASTA files	n/a	File
LSU OTU tables in HDF5 format (SILVA DB)	LSU OTU tables in HDF5 format (SILVA DB)	n/a	File
SSU OTU tables in HDF5 format (SILVA DB)	SSU OTU tables in HDF5 format (SILVA DB)	n/a	File
SSU OTU tables in JSON format (SILVA DB)	SSU OTU tables in JSON format (SILVA DB)	n/a	File
LSU taxonomic abundance pie charts (SILVA DB)	LSU taxonomic abundance pie charts (SILVA DB)	n/a	File
LSU taxonomic classifications using SILVA DB	LSU taxonomic classifications using SILVA DB	n/a	File
LSU FASTA files	LSU FASTA files	n/a	File
SSU OTU tables (SILVA DB)	SSU OTU tables (SILVA DB)	n/a	File
SSU taxonomic abundance pie charts (SILVA DB)	SSU taxonomic abundance pie charts (SILVA DB)	n/a	File
LSU OTU tables in JSON format (SILVA DB)	LSU OTU tables in JSON format (SILVA DB)	n/a	File
ITS FASTA files	ITS FASTA files	n/a	File
ITS OTU tables in JSON format (UNITE DB)	ITS OTU tables in JSON format (UNITE DB)	n/a	File
ITS OTU tables in HDF5 format (UNITE DB)	ITS OTU tables in HDF5 format (UNITE DB)	n/a	File
ITS taxonomic classifications using ITSoneDB	ITS taxonomic classifications using ITSoneDB	n/a	File
ITS OTU tables in JSON format (ITSoneDB)	ITS OTU tables in JSON format (ITSoneDB)	n/a	File
ITS OTU tables in HDF5 format (ITSoneDB)	ITS OTU tables in HDF5 format (ITSoneDB)	n/a	File
ITS OTU tables (UNITE DB)	ITS OTU tables (UNITE DB)	n/a	File
ITS taxonomic abundance pie charts (UNITE DB)	ITS taxonomic abundance pie charts (UNITE DB)	n/a	File
ITS taxonomic classifications using UNITE DB	ITS taxonomic classifications using UNITE DB	n/a	File
ITS taxonomic abundance pie charts (ITSoneDB)	ITS taxonomic abundance pie charts (ITSoneDB)	n/a	File
ITS OTU tables (ITSoneDB)	ITS OTU tables (ITSoneDB)	n/a	File
SSU phylum level taxonomic abundance summary table	SSU phylum level taxonomic abundance summary table	n/a	File
SSU taxonomic abundance summary table	SSU taxonomic abundance summary table	n/a	File
LSU phylum level taxonomic abundance summary table	LSU phylum level taxonomic abundance summary table	n/a	File
LSU taxonomic abundance summary table	LSU taxonomic abundance summary table	n/a	File
ITSoneDB taxonomic abundance summary table	ITSoneDB taxonomic abundance summary table	n/a	File
ITSoneDB phylum level taxonomic abundance summary table	ITSoneDB phylum level taxonomic abundance summary table	n/a	File
ITS UNITE DB phylum level taxonomic abundance summary table	ITS UNITE DB phylum level taxonomic abundance summary table	n/a	File
ITS UNITE DB taxonomic abundance summary table	ITS UNITE DB taxonomic abundance summary table	n/a	File

mgnify-amplicon-pipeline-v5-complete/main v0.1 (earliest) v0.2 (latest) v0.1 (earliest)