From 731e803e0927c91bc0175474571f2d84aa5d1898 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Fri, 22 Mar 2024 13:27:39 +0100 Subject: [PATCH] Fix paths --- assets/samplesheet.csv | 2 +- conf/test.config | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index c8408736..b8bd10cf 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,2 +1,2 @@ sample,file,family_id,paternal_id,maternal_id,sex,phenotype -HG002_Revio,/media/ssd_4tb/felix/projects/skierfe/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM1,XXX,YYY,1,1 +HG002_Revio,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1 diff --git a/conf/test.config b/conf/test.config index 35565cb9..f3072f03 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,21 +23,21 @@ params { // Genome references - fasta = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/test_data/hg38.test.fa.gz" - input = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/samplesheet.csv" + fasta = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/hg38.test.fa.gz" + input = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/samplesheet.csv" - bed = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/test_data.bed" + bed = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data.bed" // HiFiCNV - hificnv_xy = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/external/expected_cn.hg38.XY.bed" - hificnv_xx = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/external/expected_cn.hg38.XX.bed" - hificnv_exclude = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/test_data/empty.bed" + hificnv_xy = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/expected_cn.hg38.XY.bed" + hificnv_xx = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/expected_cn.hg38.XX.bed" + hificnv_exclude = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/empty.bed" // Dipcall - dipcall_par = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/external/hs38.PAR.bed" + dipcall_par = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/hs38.PAR.bed" // TRGT - trgt_repeats = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/assets/external/pathogenic_repeats.hg38.bed" + trgt_repeats = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/pathogenic_repeats.hg38.bed" // Not tested skip_snv_annotation = true