Workflow: rnaediting1strand.cwl

Fetched 2023-01-11 17:48:05 GMT
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Inputs

ID Type Title Doc
ct Boolean
dp String
gt Boolean
beta Integer
alpha Integer
non_ag Integer
known_snp File
reference File
single_end Boolean
edge_mutation Integer
edit_fraction Float
variants_only Boolean
keep_all_edited Boolean
junction_overhang Integer
reverse_split_bam Boolean
input_unsorted_bam File
min_variant_coverage Integer
skip_duplicate_removal Boolean
reverse_stranded_library Boolean

Steps

ID Runs Label Doc
sort
sort.cwl (CommandLineTool)
rmdup
rmdup.cwl (CommandLineTool)
mpileup
mpileup.cwl (CommandLineTool)
call_snvs
call_snvs.cwl (CommandLineTool)
rank_edits
rank_edits.cwl (CommandLineTool)
index_reads
samtools-index.cwl (CommandLineTool)

samtools-index.cwl is developed for CWL consortium

filter_reads
filter_reads.cwl (CommandLineTool)
filter_variants
filter_variants.cwl (CommandLineTool)
format_variants
format_variants.cwl (CommandLineTool)
filter_known_snp
filter_known_snp.cwl (CommandLineTool)

Outputs

ID Type Label Doc
mpileup_output File
call_snvs_output File
rmdup_bam_output File
rank_edits_output File
sorted_bam_output File
filtered_bam_output File
rank_edits_output_bed File
filter_variants_output File
format_variants_output File
filter_known_snp_output File
Permalink: https://w3id.org/cwl/view/git/8dd7b83d5252a7e9b40307a8da5e55e4bbf1f7a1/cwl/rnaediting1strand.cwl