Conditional rule with conda environment #163
Description
Hi.
Following advice given by Johannes Köster in Add complex conditional file dependency
on how to include a conditional I've got the following conditional rule
rule bowtie2_align_reads:
input:
idx = IDX,
reads = lambda wildcards: expand(join(
config["fastqdir"],
"{file}"),
file = config["units"][wildcards.sample])
output:
join(
config["analysisdir"],
"{reference_version}/alignment/{sample}.bam")
log:
"logs/bowtie2_{reference_version}_{sample}.log"
params:
cmd = config["bowtie2"]["cmd"],
ref = re.sub(".fa", "", REF),
in_fmt = config["bowtie2"]["in_fmt"],
phred = config["bowtie2"]["phred"],
maxins = config["bowtie2"]["maxins"],
mismatch = config["bowtie2"]["mismatch"],
threads = config["bowtie2"]["threads"]
version: "1.0"
run:
if (len(input.reads) == 2):
shell(" \
{params.cmd} \
{params.phred} \
--no-mixed \
--no-discordant \
--maxins {params.maxins} \
-N {params.mismatch} \
--threads {params.threads} \
-x {params.ref} \
-1 {input.reads[0]} \
-2 {input.reads[1]} \
2> {log} \
| samtools view -bS -F4 - > {output} \
")
elif (len(input.reads) == 1):
shell(" \
{params.cmd} \
{params.phred} \
-N {params.mismatch} \
--threads {params.threads} \
-x {params.ref} \
-U {input.reads} \
2> {log} \
| samtools view -bS -F4 - > {output} \
")In an attempt to "robustify" the workflow I am trying to use conda environments per rule. However, when I add
conda:
"envs/bowtie2.yaml"I get the following error
RuleException in line 42 of /home/mevers/Projects/ChIPseq_UBF_reanalysis/snakemake/rules/alignment.smk:
Conda environments are only allowed with shell, script, or wrapper directives (not with run).
My questions are:
-
Is this a bug or intended behaviour? The conditional rule uses two
shellcommands within anif-elifconstruct nested in arundirective. So while the top-level directive isrun, the actual rule decides on one of twoshellcalls. -
If this is intended behaviour, what would be the canonical way to include a conditional rule while making use of a conda environment?
Thanks,
Maurits