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hi-c-processing-bam.cwl
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hi-c-processing-bam.cwl
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---
class: "Workflow"
cwlVersion: "v1.0"
fdn_meta:
category: "filter"
data_types:
- "Hi-C"
description: "This is a subworkflow of the Hi-C data processing pipeline. It takes a bam file as input and performs parsing, sorting, filtering and deduping. It produces two output files, a lossless, filter-annotated bam file and a filtered pairs (contact list) file."
name: "hi-c-processing-bam"
title: "Hi-C Post-alignment Processing"
workflow_type: "Hi-C data analysis"
inputs:
-
fdn_format: "bam"
id: "#input_bams"
type:
-
items: "File"
type: "array"
-
fdn_format: "chromsizes"
id: "#chromsize"
type:
- "File"
-
default: 8
id: "#nthreads_parse_sort"
type:
- "int"
-
default: 8
id: "#nthreads_merge"
type:
- "int"
outputs:
-
fdn_format: "bam"
fdn_output_type: "processed"
id: "#annotated_bam"
outputSource: "#pairsam-filter/lossless_bamfile"
type:
- "File"
-
fdn_format: "pairs"
fdn_output_type: "processed"
fdn_secondary_file_formats:
- "pairs_px2"
id: "#filtered_pairs"
outputSource: "#pairsam-filter/filtered_pairs"
type:
- "File"
requirements:
-
class: "InlineJavascriptRequirement"
-
class: "ScatterFeatureRequirement"
steps:
-
fdn_step_meta:
analysis_step_types:
- "annotation"
- "sorting"
description: "Parsing and sorting bam file"
software_used:
- "pairtools_0.2.2"
id: "#pairsam-parse-sort"
in:
-
arg_name: "bam"
fdn_format: "bam"
id: "#pairsam-parse-sort/bam"
source: "#input_bams"
-
arg_name: "chromsize"
fdn_format: "chromsize"
id: "#pairsam-parse-sort/chromsize"
source: "#chromsize"
-
arg_name: "Threads"
id: "#pairsam-parse-sort/Threads"
source: "#nthreads_parse_sort"
out:
-
arg_name: "sorted_pairsam"
fdn_format: "pairsam"
id: "#pairsam-parse-sort/sorted_pairsam"
run: "pairsam-parse-sort.cwl"
scatter: "#pairsam-parse-sort/bam"
-
fdn_step_meta:
analysis_step_types:
- "merging"
description: "Merging pairsam files"
software_used:
- "pairtools_0.2.2"
id: "#pairsam-merge"
in:
-
arg_name: "input_pairsams"
fdn_format: "pairsam"
id: "#pairsam-merge/input_pairsams"
source: "#pairsam-parse-sort/sorted_pairsam"
-
arg_name: "nThreads"
id: "#pairsam-merge/nThreads"
source: "#nthreads_merge"
out:
-
arg_name: "merged_pairsam"
fdn_format: "pairsam"
id: "#pairsam-merge/merged_pairsam"
run: "pairsam-merge.cwl"
-
fdn_step_meta:
analysis_step_types:
- "filter"
description: "Marking duplicates to pairsam file"
software_used:
- "pairtools_0.2.2"
id: "#pairsam-markasdup"
in:
-
arg_name: "input_pairsam"
fdn_format: "pairsam"
id: "#pairsam-markasdup/input_pairsam"
source: "#pairsam-merge/merged_pairsam"
out:
-
arg_name: "dupmarked_pairsam"
fdn_format: "pairsam"
id: "#pairsam-markasdup/dupmarked_pairsam"
run: "pairsam-markasdup.cwl"
-
fdn_step_meta:
analysis_step_types:
- "filter"
- "file format conversion"
description: "Filtering duplicate and invalid reads"
software_used:
- "pairtools_0.2.2"
id: "#pairsam-filter"
in:
-
arg_name: "input_pairsam"
fdn_format: "pairsam"
id: "#pairsam-filter/input_pairsam"
source: "#pairsam-markasdup/dupmarked_pairsam"
-
arg_name: "chromsize"
fdn_format: "chromsize"
id: "#pairsam-filter/chromsize"
source: "#chromsize"
out:
-
arg_name: "lossless_bamfile"
fdn_format: "bam"
id: "#pairsam-filter/lossless_bamfile"
-
arg_name: "filtered_pairs"
fdn_format: "pairs"
id: "#pairsam-filter/filtered_pairs"
run: "pairsam-filter.cwl"