Merge pull request #69 from malariagen/gg_MigrateFromGotcDevToMalaria…

…genStorage Migrating all data to gs://malariagen bucket
malariagen · Dec 8, 2020 · 430efe0 · 430efe0
2 parents f2fef6f + aaef11c
commit 430efe0
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diff --git a/pipelines/SNP-genotyping-vector/gcp/input_files/small/AV0148-C.json b/pipelines/SNP-genotyping-vector/gcp/input_files/small/AV0148-C.json
@@ -1,19 +1,19 @@
 {
   "SNPGenotyping.sample_id": "AV0148-C",
   "SNPGenotyping.output_basename": "AV0148-C",
-  "SNPGenotyping.input_bam": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/AV0148-C/ShortReadAlignmentOutput/AV0148-C.bam",
-  "SNPGenotyping.input_bam_index": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/AV0148-C/ShortReadAlignmentOutput/AV0148-C.bam.bai",
-  "SNPGenotyping.alleles_vcf": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
-  "SNPGenotyping.alleles_vcf_index": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
+  "SNPGenotyping.input_bam": "gs://malariagen/ShortReadAlignment/outputs/AV0148-C/AV0148-C.bam",
+  "SNPGenotyping.input_bam_index": "gs://malariagen/ShortReadAlignment/outputs/AV0148-C/AV0148-C.bam.bai",
+  "SNPGenotyping.alleles_vcf": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
+  "SNPGenotyping.alleles_vcf_index": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
   "SNPGenotyping.reference": {
-    "ref_fasta": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
-    "ref_fasta_index": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
-    "ref_dict": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
-    "ref_sa": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
-    "ref_amb": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
-    "ref_bwt": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
-    "ref_ann": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
-    "ref_pac": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
+    "ref_fasta": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
+    "ref_fasta_index": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
+    "ref_dict": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
+    "ref_sa": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
+    "ref_amb": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
+    "ref_bwt": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
+    "ref_ann": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
+    "ref_pac": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
   },
   "SNPGenotyping.runTimeSettings": {
     "preemptible_tries": 0,
@@ -23,6 +23,8 @@
     "biobambam_docker": "us.gcr.io/broad-gotc-prod/malariagen/biobambam2:2.0.73",
     "samtools_docker": "us.gcr.io/broad-gotc-prod/malariagen/samtools:1.4.1",
     "vcftozarr_docker": "us.gcr.io/broad-gotc-prod/malariagen/samplevcftozarr:1.1",
-    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0"
+    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0",
+    "select_variants_docker": "us.gcr.io/broad-gotc-prod/malariagen/sampleselectvariants:1.0",
+    "whatshap_docker": "us.gcr.io/broad-gotc-prod/malariagen/whatshap:1.0"
   }
 }
diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/small/AV0148-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/small/AV0148-C.json
@@ -1,18 +1,18 @@
 {
   "ShortReadAlignmentAndGenotyping.sample_id": "AV0148-C",
   "ShortReadAlignmentAndGenotyping.output_basename": "AV0148-C",
-  "ShortReadAlignmentAndGenotyping.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/lanelets_gs.tsv",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
+  "ShortReadAlignmentAndGenotyping.input_file": "gs://malariagen/ShortReadAlignment/inputs/lanelets_gs_paths.tsv",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
   "ShortReadAlignmentAndGenotyping.reference": {
-    "ref_fasta": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
-    "ref_fasta_index": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
-    "ref_dict": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
-    "ref_sa": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
-    "ref_amb": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
-    "ref_bwt": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
-    "ref_ann": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
-    "ref_pac": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
+    "ref_fasta": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
+    "ref_fasta_index": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
+    "ref_dict": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
+    "ref_sa": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
+    "ref_amb": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
+    "ref_bwt": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
+    "ref_ann": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
+    "ref_pac": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
   },
   "ShortReadAlignmentAndGenotyping.runTimeSettings": {
     "preemptible_tries": 0,
@@ -22,6 +22,8 @@
     "biobambam_docker": "us.gcr.io/broad-gotc-prod/malariagen/biobambam2:2.0.73",
     "samtools_docker": "us.gcr.io/broad-gotc-prod/malariagen/samtools:1.4.1",
     "vcftozarr_docker": "us.gcr.io/broad-gotc-prod/malariagen/samplevcftozarr:1.1",
-    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0"
+    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0",
+    "select_variants_docker": "us.gcr.io/broad-gotc-prod/malariagen/sampleselectvariants:1.0",
+    "whatshap_docker": "us.gcr.io/broad-gotc-prod/malariagen/whatshap:1.0"
   }
 }
diff --git a/...lines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AA0052-C.json b/...lines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AA0052-C.json
@@ -1,17 +1,17 @@
 {
   "ShortReadAlignmentAndGenotyping.sample_id": "AA0052-C",
-  "ShortReadAlignmentAndGenotyping.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase3-validation/validation_lanelets_gcp.tsv",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
+  "ShortReadAlignmentAndGenotyping.input_file": "gs://malariagen/ShortReadAlignment/inputs/validation_lanelets_gs_paths.tsv",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
   "ShortReadAlignmentAndGenotyping.reference": {
-    "ref_fasta": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
-    "ref_fasta_index": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
-    "ref_dict": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
-    "ref_sa": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
-    "ref_amb": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
-    "ref_bwt": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
-    "ref_ann": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
-    "ref_pac": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
+    "ref_fasta": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
+    "ref_fasta_index": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
+    "ref_dict": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
+    "ref_sa": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
+    "ref_amb": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
+    "ref_bwt": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
+    "ref_ann": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
+    "ref_pac": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
   },
   "ShortReadAlignmentAndGenotyping.runTimeSettings": {
     "preemptible_tries": 0,
@@ -21,6 +21,8 @@
     "biobambam_docker": "us.gcr.io/broad-gotc-prod/malariagen/biobambam2:2.0.73",
     "samtools_docker": "us.gcr.io/broad-gotc-prod/malariagen/samtools:1.4.1",
     "vcftozarr_docker": "us.gcr.io/broad-gotc-prod/malariagen/samplevcftozarr:1.1",
-    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0"
+    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0",
+    "select_variants_docker": "us.gcr.io/broad-gotc-prod/malariagen/sampleselectvariants:1.0",
+    "whatshap_docker": "us.gcr.io/broad-gotc-prod/malariagen/whatshap:1.0"
   }
 }
diff --git a/...lines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AB0252-C.json b/...lines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AB0252-C.json
@@ -1,17 +1,17 @@
 {
   "ShortReadAlignmentAndGenotyping.sample_id": "AB0252-C",
-  "ShortReadAlignmentAndGenotyping.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase3-validation/validation_lanelets_gcp.tsv",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
-  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://broad-gotc-dev-storage/malariaGEN/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
+  "ShortReadAlignmentAndGenotyping.input_file": "gs://malariagen/ShortReadAlignment/inputs/validation_lanelets_gs_paths.tsv",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz",
+  "ShortReadAlignmentAndGenotyping.alleles_vcf_index": "gs://malariagen/references/vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz.tbi",
   "ShortReadAlignmentAndGenotyping.reference": {
-    "ref_fasta": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
-    "ref_fasta_index": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
-    "ref_dict": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
-    "ref_sa": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
-    "ref_amb": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
-    "ref_bwt": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
-    "ref_ann": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
-    "ref_pac": "gs://broad-gotc-dev-storage/malariaGEN/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
+    "ref_fasta": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
+    "ref_fasta_index": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
+    "ref_dict": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.dict",
+    "ref_sa": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.sa",
+    "ref_amb": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.amb",
+    "ref_bwt": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.bwt",
+    "ref_ann": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.ann",
+    "ref_pac": "gs://malariagen/references/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.pac"
   },
   "ShortReadAlignmentAndGenotyping.runTimeSettings": {
     "preemptible_tries": 0,
@@ -21,6 +21,8 @@
     "biobambam_docker": "us.gcr.io/broad-gotc-prod/malariagen/biobambam2:2.0.73",
     "samtools_docker": "us.gcr.io/broad-gotc-prod/malariagen/samtools:1.4.1",
     "vcftozarr_docker": "us.gcr.io/broad-gotc-prod/malariagen/samplevcftozarr:1.1",
-    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0"
+    "lftp_docker": "us.gcr.io/broad-gotc-prod/malariagen/lftp:1.0",
+    "select_variants_docker": "us.gcr.io/broad-gotc-prod/malariagen/sampleselectvariants:1.0",
+    "whatshap_docker": "us.gcr.io/broad-gotc-prod/malariagen/whatshap:1.0"
   }
 }