Workflow: wf_trim_partial_and_map_se_scatter.cwl

Fetched 2022-02-25 09:18:31 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs


ID Type Title Doc
read1s File[]
read_name String
a_adapters File
bam_suffix String
sort_names Boolean
trim_times String
dataset_name String
fastq_suffix String
trim_error_rate String
hard_trim_length Integer
speciesGenomeDir Directory
repeatElementGenomeDir Directory
trimagain_overlap_length String
trimfirst_overlap_length String


ID Runs Label Doc

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment


ID Type Label Doc
A_output_sorted_bam File[]
X_output_sorted_bam File[]
X_output_trim_first 46471cac683557e71882b2c7b0baec97[]
A_output_mapgenome_stats File[]
A_output_maprepeats_stats File[]
X_output_trim_first_metrics File[]
X_output_barcodecollapsese_bam File[]
A_output_sort_repunmapped_fastq File[]
A_output_mapgenome_star_settings File[]
A_output_maprepeats_star_settings File[]
A_output_mapgenome_mapped_to_genome File[]
A_output_maprepeats_mapped_to_genome File[]