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wf_full_IDR_pipeline_2inputs_sample.cwl
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wf_full_IDR_pipeline_2inputs_sample.cwl
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#!/usr/bin/env cwltool
doc: |
This workflow essentially restructures the inputs before sending
to wf_full_IDR_pipeline_2inputs.cwl
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
sample:
type:
# array of 2, for each rep
type: array
items:
type: record
fields:
ip_bam:
type: File
input_bam:
type: File
peak_clusters:
type: File
name:
type: string
species:
type: string
chrom_sizes:
type: File
split_peaks_bed:
type: string
default: "temp_split_IDR_peaks.bed"
split_peaks_custombed:
type: string
default: "temp_split_IDR_peaks.custombed"
rep1_merged_peaks_bed_from_cc:
type: string
default: "rep1_split_reproducible_peaks.bed"
rep1_merged_peaks_custombed_from_cc:
type: string
default: "rep1_split_reproducible_peaks.custombed"
rep2_merged_peaks_bed_from_cc:
type: string
default: "rep2_split_reproducible_peaks.bed"
rep2_merged_peaks_custombed_from_cc:
type: string
default: "rep2_split_reproducible_peaks.custombed"
outputs:
## MAPPED READ NUMBERS ##
rep1_clip_read_num:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_clip_read_num
rep2_clip_read_num:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_clip_read_num
rep1_input_read_num:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_input_read_num
rep2_input_read_num:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_input_read_num
## INPUT NORMALIZATION 1 ##
rep1_input_normed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_input_normed_bed
rep2_input_normed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_input_normed_bed
rep1_input_normed_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_input_normed_full
rep2_input_normed_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_input_normed_full
rep1_compressed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_compressed_bed
rep2_compressed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_compressed_bed
## ENTROPY FILES ##
rep1_entropy_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_entropy_full
rep2_entropy_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_entropy_full
rep1_entropy_excess_reads:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_entropy_excess_reads
rep2_entropy_excess_reads:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_entropy_excess_reads
rep1_entropy_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_entropy_bed
rep2_entropy_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_entropy_bed
## IDR OUTPUTS ##
idr_output:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/idr_output
idr_output_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/idr_output_bed
## ERICS SPLIT-JOIN PEAKS ##
rep1_idr_output_input_normed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_idr_output_input_normed_bed
rep2_idr_output_input_normed_bed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_idr_output_input_normed_bed
rep1_idr_output_input_normed_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_idr_output_input_normed_full
rep2_idr_output_input_normed_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_idr_output_input_normed_full
rep1_reproducing_peaks_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep1_reproducing_peaks_full
rep2_reproducing_peaks_full:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/rep2_reproducing_peaks_full
## FINAL OUTPUTS ##
reproducible_peaks:
type: File
outputSource:
wf_full_IDR_pipeline_2inputs/reproducible_peaks
reproducible_peaks_narrowpeak:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/reproducible_peaks_narrowpeak
reproducible_peaks_bigbed:
type: File
outputSource: wf_full_IDR_pipeline_2inputs/reproducible_peaks_bigbed
rescue_ratio:
type: File
outputSource:
wf_full_IDR_pipeline_2inputs/rescue_ratio
self_consistency_ratio:
type: File
outputSource:
wf_full_IDR_pipeline_2inputs/self_consistency_ratio
steps:
step_parse_sample_IDR:
run: parse_sample_IDR.cwl
in:
sample: sample
out: [
rep1_name,
rep1_ip_bam,
rep1_input_bam,
rep1_peak_clusters,
rep2_name,
rep2_ip_bam,
rep2_input_bam,
rep2_peak_clusters,
reproducible_peaks,
reproducible_peaks_custombed
]
wf_full_IDR_pipeline_2inputs:
run: wf_full_IDR_pipeline_2inputs.cwl
in:
rep1_name: step_parse_sample_IDR/rep1_name
rep1_clip_bam_file: step_parse_sample_IDR/rep1_ip_bam
rep1_input_bam_file: step_parse_sample_IDR/rep1_input_bam
rep1_peaks_bed_file: step_parse_sample_IDR/rep1_peak_clusters
rep2_name: step_parse_sample_IDR/rep2_name
rep2_clip_bam_file: step_parse_sample_IDR/rep2_ip_bam
rep2_input_bam_file: step_parse_sample_IDR/rep2_input_bam
rep2_peaks_bed_file: step_parse_sample_IDR/rep2_peak_clusters
species: species
chrom_sizes: chrom_sizes
merged_peaks_bed: step_parse_sample_IDR/reproducible_peaks
merged_peaks_custombed: step_parse_sample_IDR/reproducible_peaks_custombed
split_peaks_bed: split_peaks_bed
split_peaks_custombed: split_peaks_custombed
rep1_merged_peaks_bed_from_cc: rep1_merged_peaks_bed_from_cc
rep1_merged_peaks_custombed_from_cc: rep1_merged_peaks_custombed_from_cc
rep2_merged_peaks_bed_from_cc: rep2_merged_peaks_bed_from_cc
rep2_merged_peaks_custombed_from_cc: rep2_merged_peaks_custombed_from_cc
out: [
rep1_clip_read_num,
rep2_clip_read_num,
rep1_input_read_num,
rep2_input_read_num,
rep1_input_normed_bed,
rep2_input_normed_bed,
rep1_input_normed_full,
rep2_input_normed_full,
rep1_compressed_bed,
rep2_compressed_bed,
rep1_entropy_full,
rep2_entropy_full,
rep1_entropy_excess_reads,
rep2_entropy_excess_reads,
rep1_entropy_bed,
rep2_entropy_bed,
idr_output,
idr_output_bed,
rep1_idr_output_input_normed_bed,
rep2_idr_output_input_normed_bed,
rep1_idr_output_input_normed_full,
rep2_idr_output_input_normed_full,
rep1_reproducing_peaks_full,
rep2_reproducing_peaks_full,
reproducible_peaks,
reproducible_peaks_bigbed,
reproducible_peaks_narrowpeak,
rescue_ratio,
self_consistency_ratio
]