Workflow: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

Fetched 2019-09-19 10:41:16 GMT
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Inputs

ID Type Title Doc
forward_reads File [FASTQ]
reverse_reads File [FASTQ]

Steps

ID Runs Label Doc
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).

overlap_reads
../tools/seqprep.cwl (CommandLineTool)
convert_trimmed-reads_to_fasta
../tools/fastq_to_fasta.cwl (CommandLineTool)
combine_overlaped_and_unmerged_reads
../tools/seqprep-merge.cwl (CommandLineTool)
clean_fasta_headers
../tools/clean_fasta_headers.cwl (CommandLineTool)
replace problem characters from FASTA headers with dashes

Outputs

ID Type Label Doc
processed_sequences File
Permalink: https://w3id.org/cwl/view/git/cac44f2cf14110fde9951161c663c4525772f616/workflows/emg-qc-paired.cwl