mgnify-amplicon-pipeline-v5-complete/main
v0.1

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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.

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

Inputs

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?

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

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

Version History

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

Updated to v0.1


Frozen v0.1 bf4348a
help Creators and Submitter
Creators
Additional credit

EMBL's European Bioinformatics Institute

Submitter
License
Apache License 2.0
Activity

Views: 19   Downloads: 4   Runs: 0

Created: 4th Feb 2025 at 03:02

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