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main.nf
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main.nf
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nextflow.enable.dsl=2
include { seqSpecCheck_pipeline } from './seqSpecCheck_pipeline.nf'
include { seqSpecCheck_pipeline_HASHING } from './seqSpecCheck_pipeline_HASHING.nf'
include { prepare_mapping_pipeline } from './prepare_mapping_pipeline.nf'
include { mapping_rna_pipeline } from './mapping_rna_pipeline.nf'
include { mapping_guide_pipeline } from './mapping_guide_pipeline.nf'
include { mapping_hashing_pipeline } from './mapping_hashing_pipeline.nf'
include { process_mudata_pipeline_HASHING } from './process_mudata_pipeline_HASHING.nf'
include { process_mudata_pipeline } from './process_mudata_pipeline.nf'
include { evaluation_pipeline } from './evaluation_pipeline.nf'
include { dashboard_pipeline_HASHING } from './dashboard_pipeline_HASHING.nf'
include { dashboard_pipeline } from './dashboard_pipeline.nf'
workflow {
if (params.DATASET_HASHING == "true"){
seqSpecCheck_pipeline_HASHING()
}
else {
seqSpecCheck_pipeline()
}
prepare_mapping_pipeline()
mapping_rna_pipeline(
prepare_mapping_pipeline.out.parsed_covariate_file
)
mapping_guide_pipeline(
prepare_mapping_pipeline.out.parsed_covariate_file,
prepare_mapping_pipeline.out.genome
)
if (params.DATASET_HASHING == "true"){
mapping_hashing_pipeline(
prepare_mapping_pipeline.out.parsed_covariate_file,
prepare_mapping_pipeline.out.genome
)
process_mudata_pipeline_HASHING(
mapping_rna_pipeline.out.concat_anndata_rna,
mapping_rna_pipeline.out.trans_out_dir,
mapping_guide_pipeline.out.concat_anndata_guide,
mapping_guide_pipeline.out.guide_out_dir,
mapping_hashing_pipeline.out.concat_anndata_hashing,
mapping_hashing_pipeline.out.hashing_out_dir,
prepare_mapping_pipeline.out.covariate_string
)
evaluation_pipeline (
process_mudata_pipeline_HASHING.out.gencode_gtf,
process_mudata_pipeline_HASHING.out.inference_mudata
)
dashboard_pipeline_HASHING (
seqSpecCheck_pipeline_HASHING.out.guide_seqSpecCheck_plots,
seqSpecCheck_pipeline_HASHING.out.guide_position_table,
seqSpecCheck_pipeline_HASHING.out.hashing_seqSpecCheck_plots,
seqSpecCheck_pipeline_HASHING.out.hashing_position_table,
process_mudata_pipeline_HASHING.out.adata_rna,
process_mudata_pipeline_HASHING.out.filtered_anndata_rna,
mapping_rna_pipeline.out.ks_transcripts_out_dir_collected,
process_mudata_pipeline_HASHING.out.adata_guide,
mapping_guide_pipeline.out.ks_guide_out_dir_collected,
process_mudata_pipeline_HASHING.out.adata_hashing,
mapping_hashing_pipeline.out.ks_hashing_out_dir_collected,
process_mudata_pipeline_HASHING.out.adata_demux,
process_mudata_pipeline_HASHING.out.inference_mudata,
process_mudata_pipeline_HASHING.out.figures_dir,
evaluation_pipeline.out.evaluation_output_dir
)
}
else {
process_mudata_pipeline(
mapping_rna_pipeline.out.concat_anndata_rna,
mapping_rna_pipeline.out.trans_out_dir,
mapping_guide_pipeline.out.concat_anndata_guide,
mapping_guide_pipeline.out.guide_out_dir,
prepare_mapping_pipeline.out.covariate_string
)
evaluation_pipeline (
process_mudata_pipeline.out.gencode_gtf,
process_mudata_pipeline.out.inference_mudata
)
dashboard_pipeline (
seqSpecCheck_pipeline.out.guide_seqSpecCheck_plots,
seqSpecCheck_pipeline.out.guide_position_table,
process_mudata_pipeline.out.adata_rna,
process_mudata_pipeline.out.filtered_anndata_rna,
mapping_rna_pipeline.out.ks_transcripts_out_dir_collected,
process_mudata_pipeline.out.adata_guide,
mapping_guide_pipeline.out.ks_guide_out_dir_collected,
process_mudata_pipeline.out.inference_mudata,
process_mudata_pipeline.out.figures_dir,
evaluation_pipeline.out.evaluation_output_dir
)
}
}