Fix paths

genomic-medicine-sweden · Mar 22, 2024 · 731e803 · 731e803
1 parent 12ccc3f
commit 731e803
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git 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
@@ -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