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wf_clipseqcore_se_1barcode.cwl
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wf_clipseqcore_se_1barcode.cwl
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#!/usr/bin/env cwltool
### Workflow for handling reads containing one barcode ###
### Returns a bam file containing read2 only ###
cwlVersion: v1.0
class: Workflow
requirements:
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement # TODO needed?
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
#hints:
# - class: ex:ScriptRequirement
# scriptlines:
# - "#!/bin/bash"
inputs:
dataset:
type: string
speciesGenomeDir:
type: Directory
repeatElementGenomeDir:
type: Directory
# TODO: remove, we don't use it here.
species:
type: string
chrom_sizes:
type: File
# barcodesfasta:
# type: File
# randomer_length:
# type: string
read:
type:
type: record
fields:
read1:
type: File
# read2:
# type: File
adapters:
type: File
name:
type: string
# r2_bam:
# type: string
# output_bam:
# type: string
# adapters:
# type: File
### Defaults ###
# r2_bits:
# type: int
# default: 128
# is_bam:
# type: boolean
# default: true
outputs:
b1_demuxed_fastq_r1:
type: File
outputSource: demultiplex/A_output_demuxed_read1
# b1_demuxed_fastq_r2:
# type: File
# outputSource: demultiplex/A_output_demuxed_read2
b1_trimx1_fastq:
type: File[]
outputSource: b1_trim_and_map/X_output_trim_first
b1_trimx1_metrics:
type: File
outputSource: b1_trim_and_map/X_output_trim_first_metrics
b1_trimx1_fastqc_report:
type: File
outputSource: b1_trim_and_map/X_output_trim_first_fastqc_report
b1_trimx1_fastqc_stats:
type: File
outputSource: b1_trim_and_map/X_output_trim_first_fastqc_stats
b1_trimx2_fastq:
type: File[]
outputSource: b1_trim_and_map/X_output_trim_again
b1_trimx2_metrics:
type: File
outputSource: b1_trim_and_map/X_output_trim_again_metrics
b1_trimx2_fastqc_report:
type: File
outputSource: b1_trim_and_map/X_output_trim_again_fastqc_report
b1_trimx2_fastqc_stats:
type: File
outputSource: b1_trim_and_map/X_output_trim_again_fastqc_stats
b1_maprepeats_mapped_to_genome:
type: File
outputSource: b1_trim_and_map/A_output_maprepeats_mapped_to_genome
b1_maprepeats_stats:
type: File
outputSource: b1_trim_and_map/A_output_maprepeats_stats
b1_maprepeats_star_settings:
type: File
outputSource: b1_trim_and_map/A_output_maprepeats_star_settings
b1_sorted_unmapped_fastq:
type: File
outputSource: b1_trim_and_map/A_output_sort_repunmapped_fastq
b1_mapgenome_mapped_to_genome:
type: File
outputSource: b1_trim_and_map/A_output_mapgenome_mapped_to_genome
b1_mapgenome_stats:
type: File
outputSource: b1_trim_and_map/A_output_mapgenome_stats
b1_mapgenome_star_settings:
type: File
outputSource: b1_trim_and_map/A_output_mapgenome_star_settings
b1_output_pre_rmdup_sorted_bam:
type: File
outputSource: b1_trim_and_map/A_output_sorted_bam
b1_output_barcodecollapsese_metrics:
type: File
outputSource: b1_trim_and_map/X_output_barcodecollapsese_metrics
b1_output_rmdup_sorted_bam:
type: File
outputSource: b1_trim_and_map/X_output_sorted_bam
output_pos_bw:
type: File
outputSource: make_bigwigs/posbw
output_neg_bw:
type: File
outputSource: make_bigwigs/negbw
steps:
###########################################################################
# Upstream
###########################################################################
demultiplex:
run: wf_demultiplex_se.cwl
in:
dataset: dataset
read: read
out: [
A_output_demuxed_read1,
read_name,
dataset_name
]
b1_trim_and_map:
run: wf_trim_and_map_se.cwl
in:
speciesGenomeDir: speciesGenomeDir
repeatElementGenomeDir: repeatElementGenomeDir
trimfirst_overlap_length:
default: "1"
trimagain_overlap_length:
default: "5"
a_adapters:
source: read
valueFrom: |
${
return self.adapters;
}
read1: demultiplex/A_output_demuxed_read1
read_name: demultiplex/read_name
dataset_name: demultiplex/dataset_name
out: [
X_output_trim_first,
X_output_trim_first_metrics,
X_output_trim_first_fastqc_report,
X_output_trim_first_fastqc_stats,
X_output_trim_again,
X_output_trim_again_metrics,
X_output_trim_again_fastqc_report,
X_output_trim_again_fastqc_stats,
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,
# A_output_sorted_bam_index,
X_output_barcodecollapsese_bam,
X_output_barcodecollapsese_metrics,
X_output_sorted_bam
]
###########################################################################
# Downstream (candidate for merging with main pipeline)
###########################################################################
make_bigwigs:
run: makebigwigfiles.cwl
in:
chromsizes: chrom_sizes
bam: b1_trim_and_map/X_output_sorted_bam
out:
[posbw, negbw]