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03-quantification.cwl
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03-quantification.cwl
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class: Workflow
cwlVersion: v1.0
doc: DNase-seq 03 quantification
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
nthreads:
default: 1
type: int
input_pileup_bedgraphs:
type: File[]
input_bam_files:
type: File[]
input_peak_xls_files:
type: File[]
input_read_count_dedup_files:
type: File[]
input_genome_sizes:
type: File
steps:
bedsort_scaled_bdg:
run: ../quant/bedSort.cwl
in:
bed_file: scale-bedgraph/bedgraph_scaled
scatter: bed_file
out:
- bed_file_sorted
bedsort_genomecov:
run: ../quant/bedSort.cwl
in:
bed_file: bedtools_genomecov/output_bedfile
scatter: bed_file
out:
- bed_file_sorted
bdg2bw-extend-norm:
run: ../quant/bedGraphToBigWig.cwl
in:
output_suffix:
valueFrom: .fragment_extended.bw
genome_sizes: input_genome_sizes
bed_graph: bedsort_scaled_bdg/bed_file_sorted
scatter: bed_graph
out:
- output_bigwig
scale-bedgraph:
run: ../peak_calling/scale-bedgraph.cwl
in:
bedgraph_file: input_pileup_bedgraphs
read_count_file: input_read_count_dedup_files
scatterMethod: dotproduct
scatter:
- bedgraph_file
- read_count_file
out:
- bedgraph_scaled
bedsort_clipped_bedfile:
run: ../quant/bedSort.cwl
in:
bed_file: clip-off-chrom/bed_file_clipped
scatter: bed_file
out:
- bed_file_sorted
bdg2bw-raw:
run: ../quant/bedGraphToBigWig.cwl
in:
output_suffix:
valueFrom: .raw.bw
genome_sizes: input_genome_sizes
bed_graph: bedsort_genomecov/bed_file_sorted
scatter: bed_graph
out:
- output_bigwig
bedtools_genomecov:
run: ../map/bedtools-genomecov.cwl
in:
bg:
valueFrom: ${return true}
g: input_genome_sizes
ibam: input_bam_files
scatter: ibam
out:
- output_bedfile
bamcoverage:
run: ../quant/deeptools-bamcoverage.cwl
in:
numberOfProcessors: nthreads
extendReads:
valueFrom: ${return 200}
normalizeUsing:
valueFrom: RPKM
binSize:
valueFrom: ${return 50}
bam: input_bam_files
output_suffix:
valueFrom: .norm.bw
scatter: bam
out:
- output_bam_coverage
bdg2bw-extend:
run: ../quant/bedGraphToBigWig.cwl
in:
output_suffix:
valueFrom: .fragment_extended.bw
genome_sizes: input_genome_sizes
bed_graph: bedsort_clipped_bedfile/bed_file_sorted
scatter: bed_graph
out:
- output_bigwig
clip-off-chrom:
run: ../quant/bedClip.cwl
in:
bed_file: extend-reads/stdoutfile
genome_sizes: input_genome_sizes
scatter: bed_file
out:
- bed_file_clipped
extend-reads:
run: ../quant/bedtools-slop.cwl
in:
i: input_pileup_bedgraphs
b:
valueFrom: ${return 0}
g: input_genome_sizes
scatter: i
out:
- stdoutfile
outputs:
bigwig_raw_files:
doc: Raw reads bigWig (signal) files
type: File[]
outputSource: bdg2bw-raw/output_bigwig
bigwig_norm_files:
doc: Normalized reads bigWig (signal) files
type: File[]
outputSource: bamcoverage/output_bam_coverage
bigwig_extended_norm_files:
doc: Normalized fragment extended reads bigWig (signal) files
type: File[]
outputSource: bdg2bw-extend-norm/output_bigwig
bigwig_extended_files:
doc: Fragment extended reads bigWig (signal) files
type: File[]
outputSource: bdg2bw-extend/output_bigwig