set file version

genomic-medicine-sweden · Feb 16, 2024 · 608d2bc · 608d2bc
1 parent d3e6ea3
commit 608d2bc
Showing 1 changed file with 24 additions and 24 deletions.
diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml
@@ -5,61 +5,61 @@
      path: GMS560/cnv/cnv_amp_genes_hg38.bed
      checksum: 51ca611484f5b406edfe79f06e8879ef
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_amp_genes_hg38.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amp_genes_hg38.bed
 
    cnv_loh_genes_all: 
      path: GMS560/cnv/cnv_loh_genes_hg38.bed
      checksum: 219ec534eb7bf5e617a8d4d11a18ca24
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_loh_genes_hg38.bed 
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_loh_genes_hg38.bed
 
    cnv_loh_genes_validated: 
      path: GMS560/cnv/cnv_loh_uppsala_genes_hg38.bed
      checksum: 88026108ccf28766e12385a356fffd21
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_loh_uppsala_genes_hg38.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_loh_uppsala_genes_hg38.bed
 
  bcftools_filter_include_region:
    exon: 
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed
      checksum: 720e34fbe7d559980a283cc2839c559a
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed
 
  bcftools_filter_exclude_region:
    blacklist: 
      checksum: 3911faef7fd360a7960841d2ba4b6054
      path: GMS560/cnv/cnvkit_germline_blacklist_20221221_hg38.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnvkit_germline_blacklist_20221221_hg38.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnvkit_germline_blacklist_20221221_hg38.bed
 
  bcftools_id_snps:
    snps_bed: 
      checksum: 907d2ba6fcac9b33b5a4fcdef0eedb66
      path: GMS560/design/ID_SNPs_hg38.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/ID_SNPs_hg38.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/ID_SNPs_hg38.bed
 
  call_small_cnv_amplifications:
    regions_file: 
      checksum: 4f7b0d50c0acc18201512e59322c144c
      path: GMS560/cnv/cnv_amplification_genes_hg38.tsv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_amplification_genes_hg38.tsv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amplification_genes_hg38.tsv
 
  call_small_cnv_deletions:
    regions_file:
      checksum: 92510485ce32e9ef64697121aae4122c
      path: GMS560/cnv/cnv_deletion_genes_hg38.tsv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_deletion_genes_hg38.tsv 
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_deletion_genes_hg38.tsv 
 
  exon_skipping:
    design_bed:
      checksum: 75299f3690fd91d8e42e7db3743896b2
      path: GMS560/design/Twist_RNA_Design5.annotated.hg38.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Twist_RNA_Design5.annotated.hg38.bed
 
  filter_fuseq_wes:
    gene_white_list:
@@ -92,98 +92,98 @@
      checksum: 32f3be3365e485092c33e9f0997968c1
      path: GMS560/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list
 
  hotspot_annotation:
    hotspots:
      checksum: 08c574ec13984188c8e4d2c80c14d2e3
      path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Hotspots_combined_regions_nodups.231011_hg38.csv
 
  hotspot_info:
    hotspot_mutations:
      checksum: 08c574ec13984188c8e4d2c80c14d2e3
      path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Hotspots_combined_regions_nodups.231011_hg38.csv
 
  hotspot_report:
    hotspot_mutations:
      checksum: 08c574ec13984188c8e4d2c80c14d2e3
      path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Hotspots_combined_regions_nodups.231011_hg38.csv
 
  manta_config_t:
    extra:
      checksum: 15dc3d83cba8ffbb8e5226ae38b26da8
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz
    extra_tbi:
      checksum: 2c76712f672c4bf7f05eba12314ff61d
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi
      type: file        
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi
 
  purecn:    
    intervals: 
      checksum: af529c0ece5fe201de4d507000564ff7
      path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt
 
  purecn_coverage:
    intervals:
      checksum: af529c0ece5fe201de4d507000564ff7
      path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt
 
  report_fusions:
    annotation_bed:
      checksum: af529c0ece5fe201de4d507000564ff7
      path: GMS560/design/Twist_RNA_fusionpartners_hg38.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/Twist_RNA_fusionpartners.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/rna_fusion/Twist_RNA_fusionpartners.bed
 
    fp_fusions: 
      checksum: eca1c1cf1f1e068cbdada20bdb75c392
      path: GMS560/rna_fusion/filter_rna_fusions_20231024.txt
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/filter_rna_fusions_20231024.txt
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/rna_fusion/filter_rna_fusions_20231024.txt
 
  references:
    design_bed:
      checksum: ad95a96bfb3416ce6d2aadf6e3df207c
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
 
    design_intervals: 
      checksum: 86a073346c27a5c7c5034f82b79ed65c
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list
 
    design_intervals_gatk_cnv: 
      checksum: 58088e1c88e02f7b0cfd5211eabc01cd
      path: GMS560/design/gatk.design.hg38.preprocessed.interval_list
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/gatk.design.hg38.preprocessed.interval_list
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/gatk.design.hg38.preprocessed.interval_list
 
    design_bed_rna:
      checksum: ad95a96bfb3416ce6d2aadf6e3df207c
      path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed
 
    design_intervals_rna:
      checksum: 2d05715acc2a54f11e8c2ead3126d76e
      path: GMS560/design/Twist_RNA_Design5.annotated.hg38.interval_list
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.interval_list
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Twist_RNA_Design5.annotated.hg38.interval_list
 
  tmb:
    filter_genes: