dvc.lock

schema: '2.0'
stages:
  prepare_bulk:
    cmd: python gtex.py prepare-bulk
    deps:
    - path: data/gtex/input/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
      md5: 3a863b00db00a0a08a5c7900d44ea119
      size: 11512258
    - path: data/gtex/input/GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt
      md5: 90297fc31512902f4459c757180fe575
      size: 20271
    outs:
    - path: data/gtex/interim/expressions_extended.parquet
      md5: 9bd80e5c458075eedeaf8186c46dd64d
      size: 3060639498
    - path: data/gtex/interim/samples_with_subjects.parquet
      md5: 5c0b2bf69218ef69ad13662a700da3e1
      size: 5128257
  download:
    cmd: python gtex.py download
    outs:
    - path: data/gtex/input/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad
      md5: 6cdacd7628d5f74e0beaa55f148ecb79
      size: 1898884113
    - path: data/gtex/input/GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad
      md5: 724f876e6fb9d6827c93378980f57148
      size: 128359108
    - path: data/gtex/input/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm_stable.gct
      md5: 28e07358435f544d7335e43123c2fdd5
      size: 5188527799
    - path: data/gtex/input/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
      md5: 3a863b00db00a0a08a5c7900d44ea119
      size: 11512258
    - path: data/gtex/input/GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt
      md5: 90297fc31512902f4459c757180fe575
      size: 20271
    - path: data/gtex/interim/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm_stable_expressions.tsv
      md5: 3e9375f930b66d0e1374b50574ff3a25
      size: 5188527799
  train_gtex:
    cmd: python gtex.py train
    deps:
    - path: data/gtex/interim/expressions_extended.parquet
      md5: 9bd80e5c458075eedeaf8186c46dd64d
      size: 3060639498
    outs:
    - path: data/gtex/output/all/gtex_metrics_best_huber.json
      md5: 37ae7f6a76efc6048fcdbebed254fe42
      size: 80
    - path: data/gtex/output/all/gtex_metrics_best_mse.json
      md5: 37ae7f6a76efc6048fcdbebed254fe42
      size: 80
    - path: data/gtex/output/all/gtex_metrics_plot.json
      md5: 41e39c39cb1de4b99f1c2188ebbc628d
      size: 14362
  prepare_cattle:
    cmd: python gtex.py  prepare-cattle-bulk
    outs:
    - path: data/cattle/input/Gene_read_counts_FarmGTEx_cattle_V0.tsv
      md5: 6ac61cdb28173cde2211db48e7808918
      size: 649836736