Snakefile_rna_fullanalysis

#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_rna_import.smk"
## Full analysis part
include: "rules/singlecell_rna_seurat_proc.smk"
include: "rules/singlecell_rna_singleR.smk"
include: "rules/singlecell_rna_report.smk"

copy_complete = 'copy.complete'
if external == True:
    wreport_result = []
    xreport_result = []
    copy_complete = []

rule all:
    input:
        expand(os.path.join(analysis, "{sample}/singleR/seur_10x_cluster_singler.rds"), sample=samples),
        expand(os.path.join(analysis, "{sample}/seurat/seur_10x_cluster_object.rds"), sample=samples), 
        expand(os.path.join(analysis, "{sample}_sc_report.html"), sample = samples), 
        expand("run_{sample}_10x_cellranger_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