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https://github.com/arjunrajlaboratory/RajLabSeqTools
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
units.schema.yaml 
$schema: "http://json-schema.org/draft-06/schema#"
description: row of the units.tsv, representing a sequencing unit, i.e. single-end or paired-end data
type: object
properties:
  sample:
    type: string
    description: sample name/id the unit has been sequenced from
  unit:
    type: string
    description: unit id
  fq1:
    type: string
    description: path to FASTQ file
  fq2:
    type: string
    description: path to second FASTQ file (leave empty in case of single-end)
  strandedness:
    type: string
    description: one of the values '0', 'yes' or 'reverse' according to protocol strandedness
required:
  - sample
  - unit
  - fq1