Snakemake conda env parameter is not taken from config.yaml file - bioinformatics

Question

I use a conda env that I create manually, not automatically using Snakemake. I do this to keep tighter version control.
Anyway, in my config.yaml I have the following line:
conda_env: '/rst1/2017-0205_illuminaseq/scratch/swo-406/snakemake'
Then, at the start of my Snakefile I read that variable (reading variables from config in your shell part does not seem to work, am I right?):
conda_env = config['conda_env']
Then in a shell part I hail said parameter like this:
rule rsem_quantify:
input:
os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')
output:
os.path.join(analyzed_dir, '{sample}.genes.results'),
os.path.join(analyzed_dir, '{sample}.STAR.genome.bam')
threads: 8
shell:
'''
#!/bin/bash
source activate {conda_env}
rsem-calculate-expression \
--paired-end \
{input} \
{rsem_ref_base} \
{analyzed_dir}/{wildcards.sample} \
--strandedness reverse \
--num-threads {threads} \
--star \
--star-gzipped-read-file \
--star-output-genome-bam
'''
Notice the {conda_env}. Now this gives me the following error:
Could not find conda environment: None
You can list all discoverable environments with `conda info --envs`.
Now, if I change {conda_env} for its parameter directly /rst1/2017-0205_illuminaseq/scratch/swo-406/snakemake, it does work! I don't have any trouble reading other parameters using this method (like rsem_ref_base and analyzed_dir in the example rule above.
What could be wrong here?
Highest regards,
Freek.

Answer 1

The pattern I use is to load variables into params, so something along the lines of
rule rsem_quantify:
input:
os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')
output:
os.path.join(analyzed_dir, '{sample}.genes.results'),
os.path.join(analyzed_dir, '{sample}.STAR.genome.bam')
params:
conda_env=config['conda_env']
threads: 8
shell:
'''
#!/bin/bash
source activate {params.conda_env}
rsem-calculate-expression \
...
'''
Although, I'd also never do this with a conda environment, because Snakemake has conda environment management built-in. See this section in the docs on Integrated Package Management for details. This makes reproducibility much more manageable.