snakecharm
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Rule or checkpoint has not beed defined false positive
shell.executable("bash")
rule all:
input:
'result.r1',
'result.c1', # targeting checkpoint output overrides input
'result.c2'
# TODO: works OK
def rule1_input(wc):
checkpoints.check1.get(**wc).output[0]
return "result.r2"
rule r1:
input:
rule1_input
output:
'result.r1',
shell:
'echo {input} > {output}'
rule r2:
output:
'result.r2'
shell:
'echo r2 > {output}'
def check1_input(wc):
checkpoints.check2.get(**wc).output[0]
return 'result.r3'
checkpoint check1:
input:
check1_input
output:
'result.c1'
shell:
'echo c1 > {output}'
checkpoint check2:
output:
'result.c2'
shell:
'echo c2 > {output}'
rule r3:
output:
'result.r3'
shell:
'echo r3 > {output}'