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DagsHub-Datasets
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ont-open-data-dataset

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params.json 3.2 KB
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  1. {
    2. 

  2.     "sv": true,
    3. 

  3.     "mod": false,
    4. 

  4.     "snv": true,
    5. 

  5.     "bam_normal": "/media/groups/custflow/active/datasets/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam",
    6. 

  6.     "bam_tumor": "/media/groups/custflow/active/datasets/colo829_2024.03/basecalls/colo829/sup/PAU61426.d052sup4305mCG_5hmCGvHg38.bam",
    7. 

  7.     "sample_name": "COLO829",
    8. 

  8.     "ref": "/media/groups/custflow/active/datasets/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta",
    9. 

  9.     "bed": null,
    10. 

  10.     "tr_bed": null,
    11. 

  11.     "annotation": true,
    12. 

  12.     "out_dir": "/media/groups/custflow/active/sgriffiths/somvar-colo829/out",
    13. 

  13.     "ubam_map_threads": 8,
    14. 

  14.     "ubam_sort_threads": 3,
    15. 

  15.     "ubam_bam2fq_threads": 1,
    16. 

  16.     "tumor_min_coverage": 10,
    17. 

  17.     "normal_min_coverage": 10,
    18. 

  18.     "depth_window_size": 50000,
    19. 

  19.     "depth_intervals": false,
    20. 

  20.     "basecaller_cfg": "dna_r10.4.1_e8.2_400bps_sup@v4.2.0",
    21. 

  21.     "normal_vcf": null,
    22. 

  22.     "hybrid_mode_vcf": null,
    23. 

  23.     "genotyping_mode_vcf": null,
    24. 

  24.     "skip_haplotype_filter": false,
    25. 

  25.     "haplotype_filter_threads": 16,
    26. 

  26.     "ctg_name": "EMPTY",
    27. 

  27.     "include_all_ctgs": false,
    28. 

  28.     "snv_min_af": 0.05,
    29. 

  29.     "indel_min_af": 0.05,
    30. 

  30.     "min_contig_size": 0,
    31. 

  31.     "min_qual": 8,
    32. 

  32.     "min_cov": 4,
    33. 

  33.     "use_longphase": true,
    34. 

  34.     "use_longphase_intermediate": true,
    35. 

  35.     "print_ref_calls": false,
    36. 

  36.     "print_germline_calls": false,
    37. 

  37.     "germline": true,
    38. 

  38.     "phase_normal": false,
    39. 

  39.     "clairs_debug": false,
    40. 

  40.     "fast_mode": false,
    41. 

  41.     "clair3_phase_vcf": false,
    42. 

  42.     "clair3_ref_pct_full": 0.1,
    43. 

  43.     "clair3_var_pct_full": 0.7,
    44. 

  44.     "clair3_min_mq": 5,
    45. 

  45.     "GVCF": false,
    46. 

  46.     "vcf_fn": "EMPTY",
    47. 

  47.     "min_sv_length": 50,
    48. 

  48.     "nanomonsv_get_threads": 4,
    49. 

  49.     "classify_insert": false,
    50. 

  50.     "control_panel": null,
    51. 

  51.     "qv": null,
    52. 

  52.     "min_ref_support": 3,
    53. 

  53.     "genotype_sv": false,
    54. 

  54.     "force_strand": false,
    55. 

  55.     "modkit_args": null,
    56. 

  56.     "dss_threads": 1,
    57. 

  57.     "modkit_threads": 4,
    58. 

  58.     "help": false,
    59. 

  59.     "version": false,
    60. 

  60.     "aws_image_prefix": null,
    61. 

  61.     "aws_queue": null,
    62. 

  62.     "disable_ping": false,
    63. 

  63.     "monochrome_logs": false,
    64. 

  64.     "validate_params": true,
    65. 

  65.     "show_hidden_params": false,
    66. 

  66.     "schema_ignore_params": "show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf",
    67. 

  67.     "wf": {
    68. 

  68.         "example_cmd": [
    69. 

  69.             "--snv",
    70. 

  70.             "--sv",
    71. 

  71.             "--mod",
    72. 

  72.             "--sample_name MYSAMPLE",
    73. 

  73.             "--ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna",
    74. 

  74.             "--bed wf-somatic-variation-demo/demo.bed",
    75. 

  75.             "--bam_normal wf-somatic-variation-demo/demo_normal.bam",
    76. 

  76.             "--bam_tumor wf-somatic-variation-demo/demo_tumor.bam",
    77. 

  77.             "--basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2",
    78. 

  78.             "--normal_min_coverage 0",
    79. 

  79.             "--tumor_min_coverage 0"
    80. 

  80.         ],
    81. 

  81.         "container_sha": "sha18cc2ea1fae27fc772e7b728957996119c1ec81a",
    82. 

  82.         "container_snp_sha": "sha92828097d0647c44c8db3958fd5985b14af9ec3a",
    83. 

  83.         "container_sv_sha": "shaa94980c361625f0d50dcaf5bcf2abd005d57ec2c",
    84. 

  84.         "container_mod_sha": "shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb",
    85. 

  85.         "common_sha": "sha1c5febff9f75143710826498b093d9769a5edbb9",
    86. 

  86.         "snpeff_tag": "sha1acac7c26e15955ec29021b28e6ee5a5140c245e",
    87. 

  87.         "dss_sha": "sha28cc44cacad092f1b074aca3548ff8ba9b483fc0",
    88. 

  88.         "agent": null
    89. 

  89.     }
    90. 

  90. }
    91.
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Integrate AWS S3
Use S3 remote
Select bucket
Access key
Finish

Use AWS S3 as storage!

Browsing data directories saved to S3 is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Existing keys:
s3://ont-open-data
Jan 31, 2023
s3://ont-open-data/giab_lsk114_2022.12
Jan 31, 2023
s3://ont-open-data/gm24385_mod_2021.09/extra_analysis/bonito_remora
Jan 31, 2023
s3://ont-open-data/rrms_2022.07
Jan 31, 2023

Specify your S3 bucket

Access key (If needed)

Congratulations!

ont-open-data-dataset is now integrated with AWS S3!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate Google Cloud Storage
Use Google Storage
Select bucket
Upload key
Finish

Use Google Cloud Storage!

Browsing data directories saved to Google Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Google Storage bucket

Service Account Key

Congratulations!

ont-open-data-dataset is now integrated with Google Cloud Storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate Azure Cloud Storage
Use Azure Storage
Select bucket
Set key
Finish

Use Azure Cloud Storage!

Browsing data directories saved to Azure Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Azure Storage bucket

Access key (If needed)

Congratulations!

ont-open-data-dataset is now integrated with Azure Cloud Storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate S3 compatible storage
Use S3 like remote
Select bucket
Access key
Finish

Use any S3 compatible storage!

Browsing data directories saved to S3 compatible storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your S3 bucket

Bucket name cannot be the same as the repository name. Please change one of them.

Access key (If needed)

Congratulations!

ont-open-data-dataset is now integrated with your S3 compatible storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes