EMG assembly for paired end Illumina - Common Workflow Language Viewer

Workflow: EMG assembly for paired end Illumina

Fetched 2023-01-10 12:13:15 GMT

Verified with cwltool version 3.1.20221201130942

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Inputs

ID	Type	Title	Doc
mapseq_ref	File [FASTA]
forward_reads	File [FASTQ]
reverse_reads	File [FASTQ]
mapseq_taxonomies	File[]
assembly_mem_limit	Integer		in Gb
fraggenescan_model	https://w3id.org/cwl/view/git/30397448563d06c342b25a3603c97b6fff7ba7d3/tools/FragGeneScan-model.yaml#model
covariance_model_database	File

Steps

ID	Runs	Label	Doc
cmscan	../tools/infernal-cmscan.cwl (CommandLineTool)	search sequence(s) against a covariance model database	http://eddylab.org/infernal/Userguide.pdf
assembly	../tools/metaspades.cwl (CommandLineTool)	metaSPAdes: de novo metagenomics assembler	https://arxiv.org/abs/1604.03071 http://cab.spbu.ru/files/release3.10.1/manual.html#meta
extract_SSUs	../tools/esl-sfetch-manyseqs.cwl (CommandLineTool)	extract by names from an indexed sequence file	https://github.com/EddyRivasLab/easel
fraggenescan	../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/
interproscan	../tools/InterProScan5.21-60.cwl (CommandLineTool)	InterProScan: protein sequence classifier	Version 5.21-60 can be downloaded here: https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload Documentation on how to run InterProScan 5 can be found here: https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
classify_SSUs	../tools/mapseq.cwl (CommandLineTool)	MAPseq	sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. http://meringlab.org/software/mapseq/
get_SSU_coords	../tools/SSU-from-tablehits.cwl (Workflow)
index_scaffolds	../tools/esl-sfetch-index.cwl (CommandLineTool)	index a sequence file for use by esl-sfetch	https://github.com/EddyRivasLab/easel
remove_asterisks_and_reformat	../tools/esl-reformat.cwl (CommandLineTool)	normalize to fasta	normalizes input sequeces to FASTA with fixed number of sequence characters per line using esl-reformat from https://github.com/EddyRivasLab/easel

Outputs

ID	Type	Label	Doc
SSUs	File
pCDS	File
scaffolds	File
annotations	File
classifications	File

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