Snakefile

# Define common functions and variables
include: 'rules/common.smk'

#include: 'rules/PoN.smk'
include: 'rules/CellTypeReannotation.smk'
include: 'rules/SNVCalling.smk'
include: 'rules/FusionCalling.smk'
include: 'rules/CellClustering.smk'
#include: 'rules/InferCopyNumbers.smk'

# Define results working directory
workdir: config['User']['output_dir']

rule LongSom_output:
    input:
        # Reannotated cell types
        expand("CellTypeReannotation/ReannotatedCellTypes/{id}.tsv", id=IDS) if REANNO else [],
        # Final SNV set
        expand("SNVCalling/BaseCellCalling/{id}.calling.step3.tsv", id=IDS) if SCOMATIC else [],
        # Fusions
        expand("FusionCalling/Somatic/{id}.Fusions.tsv", id=IDS) if CTATFUSION else [],
        # Cell-Variants matrix
        expand("CellClustering/SingleCellGenotype/{id}.BinaryMatrix.tsv", id=IDS)if BNPC else [],
        # Clonal reconstruction
        expand("CellClustering/BnpC_output/{id}/genoCluster_posterior_mean_raw.pdf", id=IDS) if BNPC else [],
        # CNVs
        expand("InferCNV/InferCNV/{id}/infercnv.17_HMM_predHMMi6.leiden.hmm_mode-subclusters.png", id = IDS) if INFERCNV else [],
    default_target: True
    localrule: True