_config.yml

# Site title and subtitle
title: 'MISO'
subtitle: 'An open-source LIMS for NGS sequencing centres'
miso_flavour: 'OICR'
miso_colour: 'rgb(56,121,59)'

# URL to source code
codeurl: 'https://github.com/miso-lims/miso-lims'

# Keep as an empty string if served up at the root. If served up at a specific
# path (e.g. on GitHub pages) leave off the trailing slash, e.g. /my-project
baseurl: '/walkthroughs'

# URL to your MISO instance for the training tutorial
miso_url: 'http://miso.gsi.oicr.on.ca'

# Configuration for important site-specific values used in the tutorials. Make
# sure these match existing items in your MISO instance.
pipeline: 'Research'
box_size: '8x12 Storage (scannable)'
sequencer: 'D00331'
platform: 'Illumina HiSeq 2500'
platform_type: 'Illumina'
reference_genome: 'Human hg19 random'
scientific_name: 'Homo sapiens'
detailed_qc_status_good: 'Ready'
detailed_qc_status_pending: 'Not Ready'
library_type: 'Paired End'
index_kit: 'Nextera DNA Dual Index'
flowcell: 'HiSeq PE Flow Cell v4'
seq_params: 'V4 2×101'
run_scanner_run: '220120_A00469_0263_AH3YMFDSX3'
lane_qc_bad: 'Failed: Other problem'

# values only affecting plain sample mode
plain_sample1_alias: 'PROJ_S01_0001'
plain_sample2_alias: 'PROJ_S02_0001'
plain_sample3_alias: 'PROJ_S03_0001'
# samples 4 and 5 are autofilled based on incrementing pattern from 2 and 3
plain_sample6_alias: 'PROJ_S06_0001'

# values only affecting detailed sample mode
identity_class: 'Identity'
tissue_class: 'Tissue'
slide_class: 'Slide'
stock_class: 'gDNA (stock)'
aliquot_class: 'gDNA (aliquot)'
tissue_origin_1: 'Ly (Lymphocyte)'
tissue_origin_2: 'Br (Breast)'
tissue_origin_3: 'nn (Unknown)'
tissue_origin_4: 'Pa (Pancreas)'
tissue_type_1: 'R (Reference or non-tumour, non-diseased tissue sample)'
tissue_type_2: 'P (Primary Tumour)'

# values for Oxford Nanopore tutorial
ont_sequencer: 'MN16303'
ont_library_type: '1D Genomic DNA by ligation'
ont_platform: 'MinION'
ont_flowcell: 'FLO-MIN107'
ont_seq_params: 'Sequencing Run'

# Configuration for indicating who the MISO administrator is and how to contact
# them
miso_admin: 'GSI'
miso_admin_contact: 'email gsi@oicr.on.ca or file a JIRA ticket in _GSI Common_'

#--------------------------------------------------------------------------------
# Settings for Jekyll - should not need to be modified.
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markdown        : kramdown
kramdown        :
  entity_output : as_input # — is output as —
  smart_quotes  : [39, 39, 34, 34] # decimal for left/right single/double quotes
#theme: minima