X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/ee6bd1242f2519b0bea425b2232394d6fe7a1d8d..2b6b1560f886c1c09004c1f2bd3d4ca472b82963:/cwl/lightning/readme.md

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-Running tiling workflow
-===
-
-Command
----
-
-arvados-cwl-runner --submit --no-wait --project-uuid <project_uuid> fasta2numpy-wf.cwl <input_yml>
-
-For examples of input yml files, see yml/fasta2numpy-wf-100test.yml and yml/fasta2numpy-wf-0831_0315.yml
-
-Notable parameters for input yml
----
-
-fastadirs: an array of fasta directories, in our implementation, each directory consists of around 100 fasta pairs
-
-batchsize: an integer determining the batch size when running lighting-import step, e.g., for batchsize 12, we run lightning-import for 12 fasta directories together as a batch, the resulting libraries then get merged by lightning-slice
-
-matchgenome: a string pattern used for obtaining a subset of the cohort, e.g, matchgenome "ADNI|WCAP" runs tiling for all samples with "ADNI" or "WCAP" in their name, matchgenome "" runs for the entire cohort
-
-trainingsetsize: a float between 0 and 1 to determine the training set size