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snapanalysis_setup_and_analyze.cwl
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snapanalysis_setup_and_analyze.cwl
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cwlVersion: v1.1
class: Workflow
# label: A workflow that analyzes a SNAP file as outlined at: 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: "2019-12-03"
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:
encode_blacklist: File?
gene_track: File?
gene_annotation: File?
preferred_barcodes: File?
promoters: File?
input_snap: File
processes: int?
outputs:
analysis_CSV_files:
type:
type: array
items: File
outputSource: snapanalysis_analyze/CSV_files
analysis_BED_files:
type:
type: array
items: File
outputSource: snapanalysis_analyze/BED_files
analysis_PDF_files:
type:
type: array
items: File
outputSource: snapanalysis_analyze/PDF_files
analysis_RDS_objects:
type:
type: array
items: File
outputSource: snapanalysis_analyze/RDS_objects
umap_coords_csv:
type: File
outputSource: snapanalysis_analyze/umap_coords_csv
cell_by_gene_matrix:
type: File
outputSource: snapanalysis_analyze/cell_by_gene_matrix
cell_by_bin_mtx:
type: File
outputSource: snapanalysis_analyze/cell_by_bin_mtx
cell_by_bin_barcodes:
type: File
outputSource: snapanalysis_analyze/cell_by_bin_barcodes
cell_by_bin_bins:
type: File
outputSource: snapanalysis_analyze/cell_by_bin_bins
motif_CSV_files:
type:
type: array
items: File
outputSource: snapanalysis_motif/CSV_files
motif_RData_file:
type: File
outputSource: snapanalysis_motif/RData_file
cell_by_bin_h5ad:
type: File
outputSource: convert_to_h5ad/cell_by_bin_h5ad
cell_by_gene_h5ad:
type: File
outputSource: convert_to_h5ad/cell_by_gene_h5ad
steps:
snapanalysis_select_barcode:
run: analyze_snap_steps/snapanalysis_select_barcode.cwl
in:
preferred_barcodes: preferred_barcodes
out:
[selected_barcodes, barcode_PDF_files]
snapanalysis_analyze:
run: analyze_snap_steps/snapanalysis_analyze.cwl
in:
input_snap: input_snap
selected_barcodes: snapanalysis_select_barcode/selected_barcodes
encode_blacklist: encode_blacklist
gene_track: gene_track
gene_annotation: gene_annotation
promoters: promoters
processes: processes
out:
- snap_rds
- peaks_combined_bed
- CSV_files
- BED_files
- PDF_files
- RDS_objects
- umap_coords_csv
- cell_by_gene_matrix
- cell_by_bin_mtx
- cell_by_bin_barcodes
- cell_by_bin_bins
snapanalysis_add_pmat_tool:
run: analyze_snap_steps/snapanalysis_add_pmat_tool.cwl
in:
snap_file: input_snap
peak_file: snapanalysis_analyze/peaks_combined_bed
out:
[snap_file_w_peaks]
snapanalysis_motif:
run: analyze_snap_steps/snapanalysis_motif.cwl
in:
snap_file: snapanalysis_add_pmat_tool/snap_file_w_peaks
snap_rds: snapanalysis_analyze/snap_rds
out:
[CSV_files, RData_file]
convert_to_h5ad:
run: convert_to_h5ad.cwl
in:
umap_coords_csv: snapanalysis_analyze/umap_coords_csv
cell_by_gene_matrix: snapanalysis_analyze/cell_by_gene_matrix
cell_by_bin_mtx: snapanalysis_analyze/cell_by_bin_mtx
cell_by_bin_barcodes: snapanalysis_analyze/cell_by_bin_barcodes
cell_by_bin_bins: snapanalysis_analyze/cell_by_bin_bins
out:
- cell_by_bin_h5ad
- cell_by_gene_h5ad