mgnify-amplicon-pipeline-v5-quality-control-paired-end/main
v0.1

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Workflow Type: Galaxy

Quality control subworkflow for paired-end reads.

SEEK ID: https://workflowhub.eu/workflows/1272?version=1

Inputs

ID Name Description Type
Ambiguity filtering - Maximal N percentage threshold to conserve sequences #main/Ambiguity filtering - Maximal N percentage threshold to conserve sequences Maximal N percentage threshold to conserve sequences.
  • int
Length filtering - Minimum size #main/Length filtering - Minimum size Minimum sequence length.
  • int
Paired-end reads #main/Paired-end reads Paired-end reads collection.
  • array containing
    • File
Trimmomatic - LEADING #main/Trimmomatic - LEADING Minimum quality required to keep a base.
  • int
Trimmomatic - MINLEN #main/Trimmomatic - MINLEN Minimum length of reads to be kept.
  • int
Trimmomatic - SLIDINGWINDOW - Average quality required #main/Trimmomatic - SLIDINGWINDOW - Average quality required Average quality required.
  • int
Trimmomatic - SLIDINGWINDOW - Number of bases to average across #main/Trimmomatic - SLIDINGWINDOW - Number of bases to average across Number of bases to average across.
  • int
Trimmomatic - TRAILING #main/Trimmomatic - TRAILING Minimum quality required to keep a base.
  • int
fastp - Enable base correction #main/fastp - Enable base correction Enable base correction in overlapped regions.
  • boolean
fastp - Length required #main/fastp - Length required Reads shorter than this value will be discarded.
  • int
fastp - Qualified quality phred #main/fastp - Qualified quality phred The quality value that a base is qualified.
  • int
fastp - Unqualified percent limit #main/fastp - Unqualified percent limit How many percents of bases are allowed to be unqualified (0~100).
  • int

Steps

ID Name Description
12 Unzip collection __UNZIP_COLLECTION__
13 fastp filtering Filtering of forward and reverse paired-end reads. toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3
14 Merging paired-end Illumina reads (SeqPrep, modified for use with MGnify piplines) toolshed.g2.bx.psu.edu/repos/bgruening/mgnify_seqprep/mgnify_seqprep/1.2+galaxy0
15 Trimming toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2
16 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
17 Length filtering toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2
18 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
19 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
20 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
21 Ambiguity filtering toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2
22 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
23 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
24 FASTQ to FASTA toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5+galaxy2
25 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
26 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
27 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
28 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0

Outputs

ID Name Description Type
Paired-end MultiQC report #main/Paired-end MultiQC report n/a
  • File
Paired-end MultiQC statistics #main/Paired-end MultiQC statistics n/a
  • File
Paired-end post quality control FASTA files #main/Paired-end post quality control FASTA files 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 74fc45b
help Creators and Submitter
Creators
Additional credit

EMBL's European Bioinformatics Institute

Submitter
Tools
fastp
Trimmomatic
FastQC
PRINSEQ
FASTX-Toolkit
MultiQC
License
Apache License 2.0
Activity

Views: 10   Downloads: 3   Runs: 0

Created: 4th Feb 2025 at 03:02

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