CWL Workflow: EMG pipeline v3.0 (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
run_id	String
5S_model	File [HMMER format]
16S_model	File [HMMER format]
23S_model	File [HMMER format]
tRNA_model	File [HMMER format]
forward_reads	File [FASTQ]
reverse_reads	File [FASTQ]
go_summary_config	File
fraggenescan_model	https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model

ID	Runs	Label
overlap_reads	../tools/seqprep.cwl (CommandLineTool)
unified_processing	emg-pipeline-v3.cwl (Workflow)	EMG pipeline v3.0 (single end version)
combine_overlaped_and_unmerged_reads	../tools/seqprep-merge.cwl (CommandLineTool)

ID	Type	Label	Doc
tree	File
summary	File
biom_tsv	File
biom_hdf5	File
biom_json	File
ipr_reads	File
pCDS_seqs	File
5S_matches	File
go_summary	File
16S_matches	File
23S_matches	File
ipr_summary	File
krona_input	File
qc_stats_gc	File
tRNA_matches	File
actual_run_id	String
post_qc_reads	File
kingdom_counts	File
go_summary_slim	File
ipr_match_count	Integer
qc_stats_gc_bin	File
annotated_CDS_aa	File
predicted_CDS_aa	File
qc_stats_seq_len	File
qc_stats_summary	File
annotated_CDS_nuc	File
no_functions_seqs	File
otu_table_summary	File
otu_visualization	File
qc_stats_gc_pcbin	File
qc_stats_nuc_dist	File
post_qc_read_count	Integer
unannotated_CDS_aa	File
processed_sequences	File
unannotated_CDS_nuc	File
interproscan_matches	File
qc_stats_seq_len_bin	File
functional_annotations	File
qc_stats_seq_len_pbcbin	File
qiime_assigned_taxonomy	File
ipr_CDS_with_match_count	Integer
ipr_reads_with_match_count	Integer
qiime_sequences-filtered_otus	File
qiime_sequences-filtered_clusters	File