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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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Delete unwanted outputs #377

Closed evanbiederstedt closed 5 years ago

evanbiederstedt commented 5 years ago

We should do this with some due diligence to make sure we're not throwing important stuff away:

Barry wrote

""" Deleting from current output that are not mentioned above: • somatic_variants/delly • somatic_variants/mutations • somatic_variants/msisensor • somatic_variants/mutation_signatures • somatic_variants/facets_maf • facets/facets0.5.14c100pc500 • hla/ • qc/conpair • lohhla/ • somatic_variants/neoantigen/neoantigen • MarkDups/ • BQSR/ • FastP/ • Alfred/ """

but that's not very precise

evanbiederstedt commented 5 years ago

I recommend we start by only publishing into the /final_output subdirectory the "bare essentials" necessary to create Barry's outputs

CC @sivkovic about the best way to delete massive amounts of unnecessary outputs not needed for /final_output

kpjonsson commented 5 years ago

Relevant: https://github.com/nextflow-io/nextflow/blob/cli-docs/docs/cli.rst

evanbiederstedt commented 5 years ago

+1 for @kpjonsson

evanbiederstedt commented 5 years ago

Related to this: https://github.com/mskcc/vaporware/issues/536

evanbiederstedt commented 5 years ago

I feel this issue is a duplicate