CWL Workflow: EMG assembly for paired end Illumina

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
mapseq_ref	File [FASTA]
forward_reads	File (Optional) [FASTQ]
reverse_reads	File (Optional) [FASTQ]
unpaired_reads	File (Optional) [FASTQ]
mapseq_taxonomy	File
go_summary_config	File
sequencing_run_id	String
fraggenescan_model	https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model
ncRNA_other_models	File[]
ncRNA_ribosomal_models	File[]
ncRNA_other_model_clans	File
mapseq_taxonomy_otu_table	File
ncRNA_ribosomal_model_clans	File

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
unified_processing	emg-core-analysis-v4.cwl (Workflow)	EMG core analysis
discard_short_scaffolds	../tools/discard_short_seqs.cwl (CommandLineTool)	drop short seqs

ID	Type	Label	Doc
pCDS_seqs	File
scaffolds	File
go_summary	File
numberOrfs	Integer
match_count	Integer
qc_stats_gc	File
stats_reads	File
5S_sequences	File
interproscan	File
other_ncRNAs	File
readsWithOrf	File
LSU_sequences	File
SSU_sequences	File
predicted_CDS	File
go_summary_slim	File
qc_stats_gc_bin	File
qc_stats_seq_len	File
qc_stats_summary	File
no_functions_seqs	File
qc_stats_gc_pcbin	File
qc_stats_nuc_dist	File
numberReadsWithOrf	Integer
ssu_classifications	File
CDS_with_match_count	Integer
qc_stats_seq_len_bin	File
functional_annotations	File
reads_with_match_count	Integer
qc_stats_seq_len_pbcbin	File