bismark_reference is not defined in Snakefile

[mbatiuk]

Thanks for sharing your data analysis pipeline

There is an issue when performing read mapping using your pipeline

After demultiplexing into cell level fastq, Snakefile is created in each multiplex group subdirectory to perform mapping

However this error appears when performing snakemake:

"RuleException in line 97 of /scratch/batiuk/primary/fastq/p/cell_level/Lightning-5-E5/Snakefile:
NameError: The name 'bismark_reference' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}"

Snakefile is not defining bismark_reference, however it is present in mapping_config.ini and should be copied over into Snakefile

[mapping reference]
bismark_reference= /home/batiuk/genomes/mus/mus109_sun1-gfp_lambda_bs
; reference directory of bismark

Manually editing Snakefile and adding bismark_reference solves error:

bismark_reference= '/home/batiuk/genomes/mus/mus109_sun1-gfp_lambda_bs'