From e7ec180f5f362fb25773e18cda51cf32f9a0de5d Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 16 Feb 2024 10:30:35 +1100 Subject: [PATCH] Update Neo reference data paths --- conf/hmf_data.config | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/conf/hmf_data.config b/conf/hmf_data.config index 82ff1af3..f80f086a 100644 --- a/conf/hmf_data.config +++ b/conf/hmf_data.config @@ -25,7 +25,7 @@ params { // ORANGE cohort_mapping = 'orange/cohort_mapping.tsv' // Hartwig cohort RNA data - cohort_tpm_medians = 'neo/tpm_cohort/hmf_tpm_medians.csv' + cohort_tpm_medians = 'neo/tpm_cohort/hmf_tpm_medians.37.csv' cohort_percentiles = 'orange/cohort_percentiles.tsv' alt_sj_distribution = 'rna_pipeline/isofox.hmf_3444.alt_sj_cohort.37.csv' gene_exp_distribution = 'rna_pipeline/isofox.hmf_3444.gene_distribution.37.csv' @@ -77,12 +77,11 @@ params { // LILAC lilac_resources = 'dna_pipeline/immune/' // Neo - neo_resources = 'neo/' + neo_resources = 'neo/binding/' // ORANGE cohort_mapping = 'orange/cohort_mapping.tsv' - // RNA cohort data - cohort_percentiles = 'orange/cohort_percentiles.tsv' - cohort_tpm_medians = 'rna_pipeline/cohort_tpm_medians.tsv' + // Hartwig cohort RNA data + cohort_tpm_medians = 'neo/tpm_cohort/hmf_tpm_medians.38.csv' cohort_percentiles = 'orange/cohort_percentiles.tsv' alt_sj_distribution = 'rna_pipeline/isofox.hmf_3444.alt_sj_cohort.38.csv' gene_exp_distribution = 'rna_pipeline/isofox.hmf_3444.gene_distribution.38.csv'