CWL Workflow: EMG assembly for paired end Illumina

Workflow: EMG assembly for paired end Illumina

Fetched 2024-04-25 12:06:25 GMT

Verified with cwltool version 3.1.20221201130942

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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	Doc
mapseq_ref	File [FASTA]
ncRNA_models	File[]
forward_reads	File (Optional) [FASTQ]
reverse_reads	File (Optional) [FASTQ]
unpaired_reads	File (Optional) [FASTQ]
mapseq_taxonomy	File
ncRNA_model_clans	File
sequencing_run_id	String
assembly_mem_limit	Integer	in Gb
fraggenescan_model	https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/FragGeneScan-model.yaml#model

Steps

ID	Runs	Label	Doc
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
find_ncRNAs	cmsearch-multimodel.cwl (Workflow)
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
visualize_otu_counts	../tools/krona.cwl (CommandLineTool)	visualize using krona
discard_short_scaffolds	../tools/discard_short_seqs.cwl (CommandLineTool)	drop short seqs
convert_otu_counts_to_hdf5	../tools/biom-convert.cwl (CommandLineTool)
convert_otu_counts_to_json	../tools/biom-convert.cwl (CommandLineTool)
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
convert_classifications_to_otu_counts	../tools/mapseq2biom.cwl (CommandLineTool)

Outputs

ID	Type	Label	Doc
SSUs	File
pCDS	File
scaffolds	File
annotations	File
classifications	File
otu_counts_hdf5	File
otu_counts_json	File
otu_visualization	File

Permalink: https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/workflows/emg-assembly.cwl