Snakefile_spatial

#shell.executable("/bin/bash")
#shell.prefix("source /etc/profile.d/modules.sh; ")

from snakemake.utils import R
import glob
import os.path
import os
import itertools
import sys


## aggregate is set to "True" in the step below
include: "rules/singlecell_import.smk"
include: "rules/singlecell_rules_common.smk"

## if there is only one sample, there is no need to run cellrange aggr 
aggregate = getattr(config, "aggregate", True)
aggr_output4ruleall = ["aggregate.complete"] if aggregate else []

## variable `samples` is created in Snakefile_singlecell_import
if len(samples) == 1:  ## only one sample 
    aggregate = False
    aggr_output4ruleall = []

include: "rules/singlecell_spatial_import.smk"

#rule_all_append defined in Snakefile_singlecell_import

rule all:
    input: expand("run_{sample}_10x_spaceranger_count.err", sample=samples), "finalreport/metric_summary.xlsx", expand("finalreport/summaries/{sample}_web_summary.html", sample=samples), aggr_output4ruleall, wreport_result, xreport_result, "QC/" + project_name + "_multiqc.html", 'copy.complete', rule_all_append