Workflow: wf_trim_partial_and_map_se_scatter.cwl

Fetched 2022-05-28 22:19:44 GMT
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Inputs

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

Steps

ID Runs Label Doc
step_wf_trim_partial_and_map

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

Outputs

ID Type Label Doc
A_output_sorted_bam File[]
X_output_sorted_bam File[]
X_output_trim_first b98f1b8cfa8064a4b9c5db1f74c5e7fb[]
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[]
Permalink: https://w3id.org/cwl/view/git/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_trim_partial_and_map_se_scatter.cwl