Workflow: wf_rnaediting2strands.cwl

Fetched 2021-04-11 15:42:54 GMT
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Inputs

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

Steps

ID Runs Label Doc
step_bam_to_bigwig_reverse
fwd
rev
step_annotator
annotator.cwl (CommandLineTool)
step_bam_to_bigwig_forward
index_reads
samtools-index.cwl (CommandLineTool)

samtools-index.cwl is developed for CWL consortium

split_strands
split_strands.cwl (CommandLineTool)
step_combine_and_reformat
combine_and_reformat.cwl (CommandLineTool)
step_score_edits
score_edits_total_coverage.cwl (CommandLineTool)
step_calmd
samtools-calmd.cwl (CommandLineTool)

Outputs

ID Type Label Doc
rev_mpileup_output File
rev_filter_known_snp_output File
fwd_rmdup_bam_output File
fwd_filtered_bam_output File
rev_filtered_bam_output File
fwd_filter_known_snp_output File
fwd_sorted_bam_output File
fwd_bigwig File
scored_edits File
rev_rank_edits_output_bed File
rev_rmdup_bam_output File
rev_bigwig File
rev_call_snvs_output File
annotated_bedfile File
fwd_rank_edits_output File
rev_filter_variants_output File
fwd_mpileup_output File
fwd_call_snvs_output File
fwd_filter_variants_output File
rev_rank_edits_output File
combined_bedfile File
rev_format_variants_output File
fwd_rank_edits_output_bed File
fwd_format_variants_output File
rev_sorted_bam_output File
Permalink: https://w3id.org/cwl/view/git/5eb7864dd3622552dc95a927d3eb6ccf5f107745/cwl/wf_rnaediting2strands.cwl