Workflow: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
forward_reads | File [FASTQ] | ||
reverse_reads | File [FASTQ] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
overlap_reads |
../tools/seqprep.cwl
(CommandLineTool)
|
||
clean_fasta_headers |
../tools/clean_fasta_headers.cwl
(CommandLineTool)
|
replace problem characters from FASTA headers with dashes | |
trim_quality_control |
../tools/trimmomatic.cwl
(CommandLineTool)
|
Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process. Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used). |
|
convert_trimmed-reads_to_fasta |
../tools/fastq_to_fasta.cwl
(CommandLineTool)
|
||
combine_overlaped_and_unmerged_reads |
../tools/seqprep-merge.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
processed_sequences | File |
Permalink:
https://w3id.org/cwl/view/git/930a2cf6fff820c2461b42dd79d71d9379343013/workflows/emg-qc-paired.cwl