dvc.lock

schema: '2.0'
stages:
  sra_prefetch:
    cmd: mkdir -p datasets/consortium/00_download/prefetch && MX_DOCKERIMAGE="ncbi/sra-tools"
      ./docker-wrapper.sh sh ./src/shared/sra_download.sh
    deps:
    - path: ./src/shared/sra_download.sh
      hash: md5
      md5: 3c95f4a0c84ee55e7e4a33bab996c39e
      size: 123
    - path: datasets/consortium/00_download/SRR_Acc_List.txt
      hash: md5
      md5: c06f0ff46b477e6212157f6508f79dd0
      size: 1896
    outs:
    - path: datasets/consortium/00_download/prefetch
      hash: md5
      md5: e48d2b2fcbc74574be120656f6865e98.dir
      size: 125465188491
      nfiles: 158
  sra_fastq_dump:
    cmd: mkdir -p datasets/consortium/00_download/fastq && MX_DOCKERIMAGE="ncbi/sra-tools"
      ./docker-wrapper.sh sh ./src/shared/sra_fastqdump.sh
    deps:
    - path: ./src/shared/sra_fastqdump.sh
      hash: md5
      md5: 5204412da0ed007b6e8dc577ce2e872a
      size: 190
    - path: datasets/consortium/00_download/SRR_Acc_List.txt
      hash: md5
      md5: c06f0ff46b477e6212157f6508f79dd0
      size: 1896
    - path: datasets/consortium/00_download/prefetch
      hash: md5
      md5: e48d2b2fcbc74574be120656f6865e98.dir
      size: 125465188491
      nfiles: 158
    outs:
    - path: datasets/consortium/00_download/fastq
      hash: md5
      md5: de1249290b202f7a3c617cb4d2cde1aa.dir
      size: 1095819375848
      nfiles: 177
  sra_organize:
    cmd: ./docker-wrapper.sh python3 ./src/shared/sra_organize.py
    deps:
    - path: ./src/shared/sra_organize.py
      hash: md5
      md5: 98c373749f8b57e42c72c85b7b3d477f
      size: 3073
    - path: datasets/consortium/00_download/GSE234246-GPL17021_series_matrix.txt.gz
      hash: md5
      md5: 1cf10f99c4bd385bdaea1acc6cb7f641
      size: 7755
    - path: datasets/consortium/00_download/GSE234246-GPL24247_series_matrix.txt.gz
      hash: md5
      md5: 1380692d8b9bee503ce3fd1d14651133
      size: 7345
    - path: datasets/consortium/00_download/SraRunTable.txt
      hash: md5
      md5: cca84775715e39811f9010d71f77648a
      size: 5084
    - path: datasets/consortium/00_download/fastq
      hash: md5
      md5: de1249290b202f7a3c617cb4d2cde1aa.dir
      size: 1095819375848
      nfiles: 177
    outs:
    - path: datasets/consortium/C9orf72-mouse/01_received_data/cohort/sample_annotations.csv
      hash: md5
      md5: 861fa066172f3e5b1f28242e675035f9
      size: 1238
    - path: datasets/consortium/C9orf72-mouse/01_received_data/rnaseq/
      hash: md5
      md5: b4eec5dc2215344db5de49ae79d28bef.dir
      size: 26131272952
      nfiles: 20
    - path: datasets/consortium/C9orf72-mouse/01_received_data/srna/
      hash: md5
      md5: c927145662353e6baaaf3616ed4139e8.dir
      size: 9888103693
      nfiles: 20
    - path: datasets/consortium/FUS-mouse/01_received_data/cohort/sample_annotations.csv
      hash: md5
      md5: a0b52d0056634b5fc845888392be7441
      size: 1118
    - path: datasets/consortium/FUS-mouse/01_received_data/rnaseq/
      hash: md5
      md5: 3ccd8345006bd583b3f8cf22d75b1d32.dir
      size: 31859651952
      nfiles: 19
    - path: datasets/consortium/FUS-mouse/01_received_data/srna/
      hash: md5
      md5: 90054527eb5f03719dcb486eead98813.dir
      size: 21251504709
      nfiles: 38
    - path: datasets/consortium/SOD1-mouse/01_received_data/cohort/sample_annotations.csv
      hash: md5
      md5: d4a62a20b040a48e437bfd7bafb0f526
      size: 1179
    - path: datasets/consortium/SOD1-mouse/01_received_data/rnaseq/
      hash: md5
      md5: 445e2c293d0ca232f1b058da1ae00494.dir
      size: 25248107738
      nfiles: 20
    - path: datasets/consortium/SOD1-mouse/01_received_data/srna/
      hash: md5
      md5: 4cabf6fa9e2ca565652b9b2c9b1b9afa.dir
      size: 16765163811
      nfiles: 20
    - path: datasets/consortium/TDP43-mouse/01_received_data/cohort/sample_annotations.csv
      hash: md5
      md5: 9bc48222a4093ab3094eb32530b2420f
      size: 1178
    - path: datasets/consortium/TDP43-mouse/01_received_data/rnaseq/
      hash: md5
      md5: 9db95b78d2f34ae7edfaf176577da5c6.dir
      size: 27548819901
      nfiles: 20
    - path: datasets/consortium/TDP43-mouse/01_received_data/srna/
      hash: md5
      md5: a34836f7ebca892240db2bf0c89ada80.dir
      size: 17602572974
      nfiles: 20
  rnaseq_download_refs:
    cmd: ./src/rnaseq/01-download-alignment-refs.sh
    outs:
    - path: database/align-references/hsapiens/GRCh38.p13.genome.fa.gz
      hash: md5
      md5: 4f6d1cc1fb7741287c0946389fcbcbb6
      size: 889409368
    - path: database/align-references/hsapiens/GRCh38.primary_assembly.genome.fa.gz
      hash: md5
      md5: bd46ea3566caa6fc6f95748bb6cf5cc4
      size: 844691642
    - path: database/align-references/hsapiens/gencode.v37.annotation.gtf.gz
      hash: md5
      md5: 362a1ae2b59bf8a1fcbebb6d626b3a70
      size: 45208353
    - path: database/align-references/hsapiens/gencode.v37.transcripts.fa.gz
      hash: md5
      md5: 9741f0fe3dc652936b9fe6fee62cbd36
      size: 75815926
    - path: database/align-references/mmusculus/GRCm39.genome.fa.gz
      hash: md5
      md5: 8f3145b642c23bb492576c9c36b6bbc6
      size: 773872991
    - path: database/align-references/mmusculus/GRCm39.primary_assembly.genome.fa.gz
      hash: md5
      md5: a26b3a14d158c49ec774d4f18585da21
      size: 773873008
    - path: database/align-references/mmusculus/gencode.vM26.annotation.gtf.gz
      hash: md5
      md5: bda62cedca8c7268c86c2597986c8655
      size: 28242075
    - path: database/align-references/mmusculus/gencode.vM26.transcripts.fa.gz
      hash: md5
      md5: 197442d0ae09cf5f78e01aad51ea50d7
      size: 54420729