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sc_atac_seq_process_and_analyze.cwl
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sc_atac_seq_process_and_analyze.cwl
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cwlVersion: v1.2
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
inputs:
assay: string
concat_fastq_dir: Directory
input_fastq1: File
input_fastq2: File
threads: int?
outputs:
bam_file:
type: File
outputSource: align_reads/paired_end_bam
bam_index:
type: File
outputSource: align_reads/paired_end_bam_index
fragment_file:
type: File
outputSource: create_fragment_file/fragment_file
Fragment_Size_Distribution_pdf:
type: File
outputSource: analyze_with_ArchR/Fragment_Size_Distribution_pdf
TSS_by_Unique_Frags_pdf:
type: File
outputSource: analyze_with_ArchR/TSS_by_Unique_Frags_pdf
QC-Sample-FragSizes-TSSProfile_pdf:
type: File
outputSource: analyze_with_ArchR/QC-Sample-FragSizes-TSSProfile_pdf
QC-Sample-Statistics_pdf:
type: File
outputSource: analyze_with_ArchR/QC-Sample-Statistics_pdf
TSS-vs-Frags_pdf:
type: File
outputSource: analyze_with_ArchR/TSS-vs-Frags_pdf
Peak-Call-Summary_pdf:
type: File
outputSource: analyze_with_ArchR/Peak-Call-Summary_pdf
Plot-UMAP-Sample-Clusters_pdf:
type: File
outputSource: analyze_with_ArchR/Plot-UMAP-Sample-Clusters_pdf
GeneScores-Marker-Heatmap_pdf:
type: File?
outputSource: analyze_with_ArchR/GeneScores-Marker-Heatmap_pdf
Peak-Marker-Heatmap_pdf:
type: File?
outputSource: analyze_with_ArchR/Peak-Marker-Heatmap_pdf
peaks_bed:
type: File
outputSource: analyze_with_ArchR/peaks_bed
peak_markers_csv:
type: File
outputSource: analyze_with_ArchR/peak_markers_csv
gene_markers_csv:
type: File?
outputSource: analyze_with_ArchR/gene_markers_csv
cell_column_data_csv:
type: File
outputSource: analyze_with_ArchR/cell_column_data_csv
gene_row_data_csv:
type: File
outputSource: analyze_with_ArchR/gene_row_data_csv
umap_coords_clusters_csv:
type: File
outputSource: analyze_with_ArchR/umap_coords_clusters_csv
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:
adjust_barcodes:
run: adjust-barcodes.cwl
in:
assay: assay
directory:
# https://www.commonwl.org/user_guide/misc/ Connect a solo value to an input that expects an array of that type
source: [ concat_fastq_dir ]
linkMerge: merge_nested
out:
[adj_fastq_dir]
align_reads:
run: align_reads.cwl
in:
num_threads: threads
input_fastq1:
source: adjust_barcodes/adj_fastq_dir
valueFrom: |
${
return {"class": "File", "location": self.location + "/barcode_added_R1.fastq"}
}
input_fastq2:
source: adjust_barcodes/adj_fastq_dir
valueFrom: |
${
return {"class": "File", "location": self.location + "/barcode_added_R2.fastq"}
}
out: [paired_end_bam, paired_end_bam_index]
analyze_with_ArchR:
run: sc_atac_seq_analyze_steps/archr_analyze.cwl
in:
bam_file: align_reads/paired_end_bam
bam_index: align_reads/paired_end_bam_index
threads: threads
out:
- Fragment_Size_Distribution_pdf
- TSS_by_Unique_Frags_pdf
- QC-Sample-FragSizes-TSSProfile_pdf
- QC-Sample-Statistics_pdf
- TSS-vs-Frags_pdf
- Peak-Call-Summary_pdf
- Plot-UMAP-Sample-Clusters_pdf
- GeneScores-Marker-Heatmap_pdf
- Peak-Marker-Heatmap_pdf
- peaks_csv
- peaks_bed
- peak_markers_csv
- gene_markers_csv
- cell_column_data_csv
- gene_row_data_csv
- umap_coords_clusters_csv
- cell_by_gene_raw_mtx
- cell_by_gene_smoothed_hdf5
- cell_by_bin_mtx
- cell_by_bin_barcodes
- cell_by_bin_bins
create_fragment_file:
run: sc_atac_seq_process_steps/create_fragment_file.cwl
in:
input_bam: align_reads/paired_end_bam
out: [fragment_file]
convert_to_h5ad:
run: convert_to_h5ad.cwl
in:
umap_coords_csv: analyze_with_ArchR/umap_coords_clusters_csv
cell_by_gene_raw_mtx: analyze_with_ArchR/cell_by_gene_raw_mtx
cell_by_gene_smoothed_hdf5: analyze_with_ArchR/cell_by_gene_smoothed_hdf5
cell_by_bin_mtx: analyze_with_ArchR/cell_by_bin_mtx
cell_by_bin_barcodes: analyze_with_ArchR/cell_by_bin_barcodes
cell_by_bin_bins: analyze_with_ArchR/cell_by_bin_bins
out:
- cell_by_bin_h5ad
- cell_by_gene_h5ad