CWL Workflow: rnaediting2strands.workflow.cwl

This workflow is Open Source and may be reused according to the terms of: BSD 3-clause "New" or "Revised" License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
ct	Boolean
dp	String
gt	Boolean
beta	Integer
alpha	Integer
gtfdb	File
non_ag	Integer
species	String
input_bam	File
known_snp	File
reference	File
single_end	Boolean
chrom_sizes	File
edge_mutation	Integer
edit_fraction	Float
fwd_is_reverse	Boolean
rev_is_reverse	Boolean
keep_all_edited	Boolean
junction_overhang	Integer
min_variant_coverage	Integer
skip_duplicate_removal	Boolean
reverse_stranded_library	Boolean

ID	Runs	Doc
fwd	rnaediting1strand.cwl (Workflow)
rev	rnaediting1strand.cwl (Workflow)
index_reads	samtools-index.cwl (CommandLineTool)	samtools-index.cwl is developed for CWL consortium
split_strands	split_strands.cwl (CommandLineTool)
step_annotator	annotator.cwl (CommandLineTool)
step_score_edits	score_edits_total_coverage.cwl (CommandLineTool)
step_combine_and_reformat	combine_and_reformat.cwl (CommandLineTool)
step_bam_to_bigwig_forward	wf_bam_to_bigwig.cwl (Workflow)
step_bam_to_bigwig_reverse	wf_bam_to_bigwig.cwl (Workflow)

ID	Type	Label	Doc
fwd_bigwig	File
rev_bigwig	File
scored_edits	File
combined_bedfile	File
annotated_bedfile	File
fwd_mpileup_output	File
rev_mpileup_output	File
fwd_call_snvs_output	File
fwd_rmdup_bam_output	File
rev_call_snvs_output	File
rev_rmdup_bam_output	File
fwd_rank_edits_output	File
fwd_sorted_bam_output	File
rev_rank_edits_output	File
rev_sorted_bam_output	File
fwd_filtered_bam_output	File
rev_filtered_bam_output	File
fwd_rank_edits_output_bed	File
rev_rank_edits_output_bed	File
fwd_filter_variants_output	File
fwd_format_variants_output	File
rev_filter_variants_output	File
rev_format_variants_output	File
fwd_filter_known_snp_output	File
rev_filter_known_snp_output	File