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10 December 2020, 08:13:14 UTC
Revision c5b88eb5aa3fa9f6a657d8b078405ce82f7e0e2d authored by Eric Sanford on 09 October 2019, 20:53:45 UTC, committed by Eric Sanford on 09 October 2019, 20:53:45 UTC
Updated STAR version, set default reference genome to hg38, added gene_names from gtf file when there is no HGNC symbol match, made it easier to change the reference genome by defining it in the setEnvironmentVariables.sh script. Modified some snakemake files to make that alternate pipeline almost runnable on the cluster in an interactive node.
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Tip revision: c5b88eb5aa3fa9f6a657d8b078405ce82f7e0e2d authored by Eric Sanford on 09 October 2019, 20:53:45 UTC
Updated STAR version, set default reference genome to hg38, added gene_names from gtf file when there is no HGNC symbol match, made it easier to change the reference genome by defining it in the setEnvironmentVariables.sh script. Modified some snakemake files to make that alternate pipeline almost runnable on the cluster in an interactive node.
Tip revision: c5b88eb
config.schema.yaml 
$schema: "http://json-schema.org/draft-06/schema#"

description: snakemake configuration file

type: object

properties:
  samples:
    type: string
  units:
    type: string
  trimming:
    type: object
    properties:
      skip:
        type: boolean
      adapter:
        type: string
        pattern: "^[ACGT]+$"

  ref:
    type: object
    properties:
      index:
        type: string
      annotation:
        type: string
    required:
      - index
      - annotation

  pca:
    type: object
    properties:
      labels:
        type: array
        items:
          type: string
    required:
      - labels

  diffexp:
    type: object
    properties:
      contrasts:
        type: object
    required:
      - contrasts

  params:
    type: object
    properties:
      star: 
        type: string
      cutadapt-se:
        type: string
      cutadapt-pe:
        type: string
    required:
      - star
      - cutadapt-se
      - cutadapt-pe

required:
  - samples
  - units
  - trimming
  - ref
  - pca
  - diffexp
  - params