Workflow: Quality assessment, amplicon classification and functional prediction

Fetched 2023-04-17 21:26:16 GMT

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

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Workflow as SVG
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  • Default Values
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  • Inputs/Outputs

Inputs

ID Type Title Doc
sample String Sample name

Name of the sample being analysed
threads Integer (Optional) number of threads

number of threads to use for computational processes
fragment String Subfragment name

Subfragment that is being analysed (e.g. V1-V3 or V5-region)
metadata File (Optional) Metadata file

UNLOCK assay metadata file
destination String (Optional) Output Destination

Optional Output destination used for cwl-prov reporting.
for_read_len Integer Reverse read length

Read length of the reverse read
reference_db String (Optional) Reference database

Reference database used in FASTA format
rev_read_len Integer (Optional) Reverse read length

Read length of the reverse read
forward_reads File forward reads

forward sequence file locally
reverse_reads File (Optional) reverse reads

reverse sequence file locally
forward_primer String Forward primer

Forward primer used
primersRemoved Boolean (Optional) Primers are removed

Wether the primers are removed or not from the input files
reverse_primer String (Optional) Reverse primer

Reverse primer used

Steps

ID Runs Label Doc
ngtax
../ngtax/ngtax.cwl (CommandLineTool)
NGTax amplicon analysis

Runs NGTAX amplicon analysis

fastqc
../fastqc/fastqc.cwl (CommandLineTool)
FASTQC

Performs quality control on FASTQ files

picrust2
../picrust2/picrust2_pipeline.cwl (CommandLineTool)
PICRUSt2 pipeline

Runs the PICRUSt2 pipeline workflow which is installed according to the following procedure:

source /root/miniconda/bin/activate && \ cd /unlock/infrastructure/conda/picrust2_v2.4.2 && \ conda env create -f /conda/picrust2_env.yml -p /unlock/infrastructure/conda/picrust2_v2.4.2 && \ conda activate /unlock/infrastructure/conda/picrust2_v2.4.2 && \ pip install --editable . && \

The folder can be obtained from the picrust2 repository.

reads_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

folder_compression
../bash/compress_directory.cwl (CommandLineTool)
Compress a directory (tar)
ngtax_to_tsv-fasta
../ngtax/ngtax_to_tsv-fasta.cwl (CommandLineTool)

NGtax2 output conversion to prepare for biom file and ASV fasta file

ngtax_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

fastqc_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

picrust_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

phyloseq_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

Outputs

ID Type Label Doc
turtle File

Used for other workflows
files_to_folder_ngtax Directory
files_to_folder_fastqc Directory
files_to_folder_phyloseq Directory
files_to_folder_picrust2 Directory
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_ngtax_picrust2.cwl