Why can't we run conda and run together in a rule? #1619
Description
Conda environments are only allowed with shell, script, notebook, or wrapper directives (not with run or template_engine).I'm receiving the above error when I'm trying to run a snakemake rule something like this
rule bcftools_consensus_1_15_1:
input:
file = rules.gatk_haplotype_caller_4_2_6_1.output.file,
reference = "resources/reference/NC_045512.2.fna",
output:
file = "output/bcftools/A_consensus.fasta",
threads: 1
conda: "env.yaml"
log: "output/bcftools/consensus_1_15_1.log"
run:
# few python statements run here
# ...
# ...
shell(
'''
bcftools consensus -f {input.reference} {input.file} \
-o {output.file} && sed -i "1s/.*/>A_fasta/" {output.file}
'''
)Is there a way to achieve the use of conda and run together??