Merge pull request #464 from genomic-medicine-sweden/PoN_figshare

feat: new PoN on figshare
genomic-medicine-sweden · May 31, 2024 · 9b3af42 · 9b3af42
2 parents 877613a + 41f3f0b
commit 9b3af42
Show file tree

Hide file tree

Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml
@@ -61,7 +61,7 @@ call_small_cnv_amplifications:
   regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_240307.tsv"
 
 cnvkit_batch:
-  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_36.cnn"
+  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg19.cnn"
 
 cnvkit_batch_hrd:
   normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_27_HRD.cnn"

diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml
@@ -61,7 +61,7 @@ call_small_cnv_amplifications:
   regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv"
 
 cnvkit_batch:
-  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn"
+  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg38.cnn"
 
 cnvkit_batch_hrd:
   normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn"

diff --git a/config/references/nextseq.hg19.pon.yaml b/config/references/nextseq.hg19.pon.yaml
@@ -30,10 +30,10 @@
 
  cnvkit_batch:
    normal_reference:
-     checksum: 2c8f519a872d92ec1cb43bd29518a71b
-     path: GMS560/PoN/cnvkit_nextseq_36.cnn
+     checksum: 203d8e695b6324f8a5c27e2c7882f3d2
+     path: GMS560/PoN/cnvkit_PoN_combined_hg19.cnn
      type: file
-     url: https://figshare.scilifelab.se/ndownloader/files/40882850
+     url: https://figshare.com/ndownloader/files/46640134?private_link=88202740beb6fcbac09d
 
  cnvkit_batch_hrd:
    normal_reference_hrd:

diff --git a/config/references/nextseq.hg38.pon.yaml b/config/references/nextseq.hg38.pon.yaml
@@ -30,10 +30,10 @@
 
  cnvkit_batch:
    normal_reference:
-     checksum: b9995ea0cfa1c259fe7229aee1fd2646
-     path: GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn
+     checksum: 0dd2ecd2e4bd4bd364404740b0f7a16c
+     path: GMS560/PoN/cnvkit_PoN_combined_hg38.cnn
      type: file
-     url: https://figshare.com/ndownloader/files/44328734?private_link=53f1597211477d840a29
+     url: https://figshare.com/ndownloader/files/46640131?private_link=88202740beb6fcbac09d
 
  #cnvkit_batch_hrd:
  #  normal_reference_hrd:

diff --git a/config/references/novaseq.hg19.pon.yaml b/config/references/novaseq.hg19.pon.yaml
@@ -29,10 +29,10 @@
 
  cnvkit_batch:
    normal_reference:
-     checksum: e7853030e7a6b0ccbeffb7c008983a29
-     path: GMS560/PoN/cnvkit_novaseq_13.cnn
+     checksum: 203d8e695b6324f8a5c27e2c7882f3d2
+     path: GMS560/PoN/cnvkit_PoN_combined_hg19.cnn
      type: file
-     url: https://figshare.scilifelab.se/ndownloader/files/40882853
+     url: https://figshare.com/ndownloader/files/46640134?private_link=88202740beb6fcbac09d
 
  cnvkit_batch_hrd:
    normal_reference_hrd: