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config.yaml
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config.yaml
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# Save the project name
project: "20190904_mixcr_pipeline"
# The directories of derived and metadata
der_dir: /cluster/project/reddy/OAS/derived_data/20190904_mixcr_pipeline
fasta_dir: /cluster/project/reddy/OAS/nucleotides
json_dir: /cluster/project/reddy/OAS/json
align_dir: /cluster/project/reddy/OAS/alignments/20190904_mixcr_pipeline
# Select the name of all files used for alignment
dirs: [
"Banerjee_2017", "Bashford_2013", "Bhiman_2015", "Bonsignori_2016",
"Briney_2019", "Collins_2015", "Corcoran_2016", "Cui_2016", "Doria-Rose_2015",
"Ellebedy_2016", "Fisher_2017", "Galson_2015", "Galson_2015a", "Galson_2016",
"Galson_2016a", "Greiff_2014", "Greiff_2015", "Greiff_2017", "Gupta_2017",
"Halliley_2015", "Huang_2016", "Jiang_2013", "Johnson_2018", "Joyce_2016",
"Khan_2016", "Levin_2015", "Levin_2017", "Li_2017", "Liao_2013", "Lindner_2015",
"Meng_2017a", "Menzel_2014", "Mroczek_2014", "Ota_2010", "Palanichamy_2014",
"Parameswaran_2014", "Pei_2017", "Prohaska_2018", "Rettig_2018", "Rubelt_2016",
"Schanz_2014", "Setliff_2018a", "Sheng_2017", "Soto_2016", "Stern_2014",
"Sundling_2014", "Thornqvist_2018", "Tipton_2015", "Turchaninova_2016",
"VanDuijn_2017", "Vander_Heiden_2017", "Vergani_2017", "Wesemann_2013",
"Wu_2011", "Wu_2014", "Wu_2015", "Zhou_2013", "Zhou_2015", "Zhu_2012", "Zhu_2013"
]
# The chains that are exported at the end of the MiXCR alignment step
# If this is changed, then the MiXCR analyze command must be changed
# as well accordingly
chains: [
"IGH", "IGL", "IGK"
]