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63 lines (48 loc) · 1.8 KB
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# include all filespace definitions
from files.sexbias_files import *
configfile: "config/config.yaml"
##### load rules #####
include: "rules/common.smk"
exclude = ['testis', 'ovary', 'male_reproductive_glands',
'gonad',
'all',
'test',
# 'antenna', 'head',
# 'body',
]
samples = samples.query("tissue not in @exclude")
#print(samples[["tissue", "resols"]])
##samples = samples.query("tissue in ['leg', 'malpighian_tubule']")
##samples = samples.query("tissue in ['leg']")
##samples = samples.query("tissue in ['testis', 'ovary']")
##samples = samples.query("tissue in ['gonad']")
#samples = samples.query("tissue in ['malpighian_tubule']")
#samples = samples.query("tissue in ['test']")
#samples = samples.query("tissue in ['body', 'malpighian_tubule']")
#samples = samples.query("tissue in ['body', 'head', 'test']")
#samples = samples.query("tissue in ['body', 'head']")
#samples = samples.query("tissue in ['body']")
#samples = samples.query("tissue in ['oenocyte']")
#samples = samples.query("tissue in ['antenna']")
#samples = samples.query("tissue in ['fat_body']")
#samples = samples.query("tissue in ['heart']")
#samples = samples.query("tissue in ['all']")
tasks = samples.explode("resols").explode("cellfilts")
#include: "rules/get_loom.smk"
#include: "rules/prepare_expression_h5ad.smk"
##include: "rules/run_scpopcorn.smk"
##include: "rules/integrate_scpopcorn_results.smk"
include: "rules/sexbias.smk"
#include: "rules/mphate.smk"
##include: "rules/markers.smk"
#include: "rules/extract_ribosomal_expr.smk"
include: "rules/fig1.smk"
#include: "rules/fig2.smk"
include: "rules/dsx_targets.smk"
#include: "rules/extra.smk"
include: "rules/copy_to_box.smk"
print(get_final_output())
##### target rules #####
rule all:
input:
get_final_output(),