/
wf_trim_partial_and_map_se_scatter.cwl
executable file
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wf_trim_partial_and_map_se_scatter.cwl
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#!/usr/bin/env cwltool
### This sub workflow should be identical to wf_trim_and_map_se.cwl except that it runs cutadapt only once. ###
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement # TODO needed?
- class: MultipleInputFeatureRequirement
#hints:
# - class: ex:ScriptRequirement
# scriptlines:
# - "#!/bin/bash"
inputs:
speciesGenomeDir:
type: Directory
repeatElementGenomeDir:
type: Directory
trimfirst_overlap_length:
type: string
trimagain_overlap_length:
type: string
# g_adapters:
# type: File
# g_adapters_default:
# type: File
a_adapters:
type: File
# a_adapters_default:
# type: File
# A_adapters:
# type: File
read1s:
type: File[]
read_name:
type: string
dataset_name:
type: string
## Defaults (don't change unless we have a very good reason) ##
sort_names:
type: boolean
default: true
trim_times:
type: string
default: "1"
trim_error_rate:
type: string
default: "0.1"
fastq_suffix:
type: string
default: ".fq"
bam_suffix:
type: string
default: ".bam"
hard_trim_length:
type: int
default: -9
outputs:
X_output_trim_first:
type:
type: array
items:
type: array
items: File
outputSource: step_wf_trim_partial_and_map/X_output_trim_first
X_output_trim_first_metrics:
type: File[]
outputSource: step_wf_trim_partial_and_map/X_output_trim_first_metrics
A_output_maprepeats_mapped_to_genome:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_maprepeats_mapped_to_genome
A_output_maprepeats_stats:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_maprepeats_stats
A_output_maprepeats_star_settings:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_maprepeats_star_settings
A_output_sort_repunmapped_fastq:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_sort_repunmapped_fastq
A_output_mapgenome_mapped_to_genome:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_mapgenome_mapped_to_genome
A_output_mapgenome_stats:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_mapgenome_stats
A_output_mapgenome_star_settings:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_mapgenome_star_settings
A_output_sorted_bam:
type: File[]
outputSource: step_wf_trim_partial_and_map/A_output_sorted_bam
X_output_barcodecollapsese_bam:
type: File[]
outputSource: step_wf_trim_partial_and_map/X_output_barcodecollapsese_bam
# X_output_barcodecollapsese_metrics:
# type: File[]
# outputSource: step_wf_trim_partial_and_map/X_output_barcodecollapsese_metrics
X_output_sorted_bam:
type: File[]
outputSource: step_wf_trim_partial_and_map/X_output_sorted_bam
steps:
step_wf_trim_partial_and_map:
run: wf_trim_partial_and_map_se.cwl
scatter: read1
in:
read1: read1s
read_name: read_name
dataset_name: dataset_name
speciesGenomeDir: speciesGenomeDir
repeatElementGenomeDir: repeatElementGenomeDir
trimfirst_overlap_length: trimfirst_overlap_length
trimagain_overlap_length: trimagain_overlap_length
a_adapters: a_adapters
out:
- X_output_trim_first
- X_output_trim_first_metrics
- A_output_maprepeats_mapped_to_genome
- A_output_maprepeats_stats
- A_output_maprepeats_star_settings
- A_output_sort_repunmapped_fastq
- A_output_mapgenome_mapped_to_genome
- A_output_mapgenome_stats
- A_output_mapgenome_star_settings
- A_output_sorted_bam
- X_output_barcodecollapsese_bam
- X_output_sorted_bam
# - X_output_barcodecollapsese_metrics