Workflow: EMG pipeline v3.0 (single end version)

Fetched 2022-10-03 04:26:04 GMT
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Inputs

ID Type Title Doc
reads File [FASTQ]
5S_model File [HMMER format]
16S_model File [HMMER format]
23S_model File [HMMER format]
tRNA_model File [HMMER format]
go_summary_config File
fraggenescan_model https://w3id.org/cwl/view/git/0cf06f13527b380d21d0f335aaea3e564094ed8f/tools/FragGeneScan-model.yaml#model

Steps

ID Runs Label Doc
ORF_prediction
../tools/FragGeneScan1_20.cwl (CommandLineTool)
FragGeneScan: find (fragmented) genes in short reads

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013 (https://sourceforge.net/projects/fraggenescan/).

Version 1.20 can be downloaded here: https://sourceforge.net/projects/fraggenescan/files/

find_SSUs_and_mask
rna-selector.cwl (Workflow)
RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

functional_analysis functional analysis prediction with InterProScan
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).

16S_taxonomic_analysis Functional analyis of sequences that match the 16S SSU
convert_trimmed-reads_to_fasta
../tools/fastq_to_fasta.cwl (CommandLineTool)

Outputs

ID Type Label Doc
tree File
biom_json File
go_summary File
predicted_CDS File
otu_table_summary File
processed_sequences File
functional_annotations File
Permalink: https://w3id.org/cwl/view/git/0cf06f13527b380d21d0f335aaea3e564094ed8f/workflows/emg-pipeline-v3.cwl