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create_snap_and_analyze.cwl
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create_snap_and_analyze.cwl
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cwlVersion: v1.1
class: Workflow
# label: A workflow that creates and analyzes a SNAP file as outlined at:
# https://github.com/r3fang/SnapTools and https://github.com/r3fang/SnapATAC
# doc: A workflow that analyzes a SNAP file as outlined at: https://github.com/r3fang/SnapATAC
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0001-5173-4627
s:email: jshands@ucsc.edu
s:name: Walter Shands
s:codeRepository: https://github.com/wshands/SnapATAC/tree/feature/snap-analysis
s:dateCreated: "2020-02-15"
s:license: https://spdx.org/licenses/Apache-2.0
s:keywords: edam:topic_0091 , edam:topic_0622
s:programmingLanguage: Python
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
$schemas:
- https://schema.org/docs/schema_org_rdfa.html
- http://edamontology.org/EDAM_1.18.owl
inputs:
reference_genome_fasta: File?
alignment_index: File?
size_index: File?
genome_name: string?
sequence_directory: Directory
blacklist_bed: File?
tmp_folder: string?
bin_size_list: int[]?
encode_blacklist: File?
gene_track: File?
gene_annotation: File?
preferred_barcodes: File?
promoters: File?
threads: int?
outputs:
zipped_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/zipped_files
report_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/report_files
fragment_file:
type: File[]
outputSource: create_and_analyze_snap_file/fragment_file
bam_file:
type: File[]
outputSource: create_and_analyze_snap_file/bam_file
alignment_qc_report:
type: File[]
outputSource: create_and_analyze_snap_file/alignment_qc_report
snap_file:
type: File[]
outputSource: create_and_analyze_snap_file/snap_file
snap_qc_file:
type: File[]
outputSource: create_and_analyze_snap_file/snap_qc_file
analysis_CSV_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_CSV_files
analysis_BED_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_BED_files
analysis_PDF_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_PDF_files
analysis_RDS_objects:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_RDS_objects
analysis_TXT_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_TXT_files
analysis_MTX_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_MTX_files
analysis_HDF5_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/analysis_HDF5_files
motif_CSV_files:
type:
type: array
items:
type: array
items: File
outputSource: create_and_analyze_snap_file/motif_CSV_files
motif_RData_file:
type:
type: array
items: File
outputSource: create_and_analyze_snap_file/motif_RData_file
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
steps:
gather_sequence_bundles:
run: gather_sequence_bundles.cwl
in:
sequence_directory: sequence_directory
out:
[fastq1_files, fastq2_files, barcode_fastq_files]
create_and_analyze_snap_file:
scatter: [input_fastq1, input_fastq2, input_barcode_fastq]
scatterMethod: dotproduct
run: steps/snaptools_create_snap_file.cwl
in:
reference_genome_fasta: reference_genome_fasta
alignment_index: alignment_index
size_index: size_index
genome_name: genome_name
input_fastq1: gather_sequence_bundles/fastq1_files
input_fastq2: gather_sequence_bundles/fastq2_files
input_barcode_fastq: gather_sequence_bundles/barcode_fastq_files
blacklist_bed: blacklist_bed
tmp_folder: tmp_folder
threads: threads
processes: threads
bin_size_list: bin_size_list
preferred_barcodes: preferred_barcodes
encode_blacklist: encode_blacklist
gene_track: gene_track
gene_annotation: gene_annotation
promoters: promoters
out:
[zipped_files, report_files, bam_file, alignment_qc_report, fragment_file, snap_file, snap_qc_file,
analysis_CSV_files, analysis_BED_files, analysis_PDF_files, analysis_HDF5_files,
analysis_RDS_objects, analysis_TXT_files, analysis_MTX_files,
motif_CSV_files, motif_RData_file]