CWL Workflow: EMG pipeline v4.0 (paired end version)

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 [FASTQ]
reverse_reads	File [FASTQ]
mapseq_taxonomy	File
go_summary_config	File
sequencing_run_id	String
fraggenescan_model	https://w3id.org/cwl/view/git/ecf044f3a5a7589cb2238487a19f22863c2bcdb1/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
overlap_reads	../tools/seqprep.cwl (CommandLineTool)
unified_processing	emg-core-analysis-v4.cwl (Workflow)	EMG core analysis
trim_and_reformat_reads	trim_and_reformat_reads.cwl (Workflow)	Trim and reformat reads (single and paired end version)
combine_overlaped_and_unmerged_reads	../tools/seqprep-merge.cwl (CommandLineTool)

ID	Type	Label	Doc
pCDS_seqs	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
processed_nucleotide_reads	File