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LCR-BCCRC / lcr-modules

Collection of standard analytical pipelines for genomic and transcriptomic data
https://lcr-modules.rtfd.io
MIT License
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Fix assertion errors #310

Closed lkhilton closed 3 months ago

lkhilton commented 4 months ago

The new Reference Workflow rules for oncodriveclustl were producing a series of assertion errors in unrelated modules (i.e. while trying to run battenberg in GAMBL). I made these changes to address those errors - @mannycruz can you please test these out in the context of your module and make sure this is still working correctly? Are the files you're working with being written or hardlinked to lcr-modules-references/genomes/grch37?

mannycruz commented 4 months ago

I added some updates to the oncodriveclustl.smk code so the file paths would match up with the changes added in reference files workflow. I tested it in smaller cohort so the workflow wouldn't take so long and it worked! Output results were created correctly so I believe it is now compatible!

I am wondering what the provider parameter is required for, I see it used in other sections in the reference_files.smk but i am not quire sure what it does in this context

rule download_oncodrive_refs: output: refs = "downloads/oncodrive/{version}/datasets/genomereference/{oncodrive_build}.master", stops = "downloads/oncodrive/{version}/datasets/genestops/{oncodrive_build}.master" params: outdir = "downloads/oncodrive/{version}/", provider = lambda w: config["genome_builds"][w.version]["provider"] conda: CONDA_ENVS["oncodriveclustl"] shell: op.as_one_line(""" export BGDATA_LOCAL={params.outdir} && bgdata get datasets/genomereference/{wildcards.oncodrive_build} && bgdata get datasets/genomereference/{wildcards.oncodrive_build} && bgdata get datasets/genestops/{wildcards.oncodrive_build} && bgdata get datasets/genestops/{wildcards.oncodrive_build} """)