From aaef11c49f181fdf7f5d1fd1c1f48d3ef229f0e9 Mon Sep 17 00:00:00 2001 From: gbggrant Date: Fri, 4 Dec 2020 10:27:07 -0500 Subject: [PATCH] Switched all gcp workflow input data to use reference data in gs://malariagen bucket. Switched all ShortReadAlignment input data to use gs://malariagen locations. Switched all SNPGenotyping input data to use gs://malariagen locations. Switched all ShortReadAlignmentAndGenotyping workflows to use gs://malariagen locations. --- .../gcp/input_files/small/AV0148-C.json | 28 ++++++++++--------- .../gcp/input_files/small/AV0148-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AA0052-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AB0252-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AC0010-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AJ0037-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AN0131-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AN0280-Cx.json | 26 +++++++++-------- .../gcp/input_files/validation/AN0326-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AR0078-C.json | 26 +++++++++-------- .../gcp/input_files/validation/AZ0156-C.json | 26 +++++++++-------- .../gcp/input_files/validation/BL0358-C.json | 26 +++++++++-------- .../gcp/input_files/AB0252-C.json | 22 ++++++++------- .../gcp/input_files/AN0131-C.json | 22 ++++++++------- .../gcp/input_files/small/AV0079-C.json | 22 ++++++++------- .../input_files/small/AV0148-C-fastqs.json | 25 ----------------- .../gcp/input_files/small/AV0148-C.json | 22 ++++++++------- 17 files changed, 217 insertions(+), 210 deletions(-) delete mode 100644 pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C-fastqs.json 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 index a450d54f..1e72a9ed 100644 --- 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" } } \ No newline at end of file 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 index 77f93349..a5f71fc4 100644 --- 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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AA0052-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AA0052-C.json index 27c2be50..fa645a82 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AA0052-C.json +++ b/pipelines/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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AB0252-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AB0252-C.json index eca45440..fb0bdf18 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AB0252-C.json +++ b/pipelines/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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AC0010-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AC0010-C.json index ef89e522..c285ad6f 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AC0010-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AC0010-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AC0010-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AJ0037-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AJ0037-C.json index 30e3ebb9..fac08fa5 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AJ0037-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AJ0037-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AJ0037-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0131-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0131-C.json index a9def9ff..57c248f3 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0131-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0131-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AN0131-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0280-Cx.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0280-Cx.json index de1454b3..ded35012 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0280-Cx.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0280-Cx.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AN0280-Cx", - "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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0326-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0326-C.json index 658cf5ca..83b8a858 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0326-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AN0326-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AN0326-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AR0078-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AR0078-C.json index a42820d8..581b6cd4 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AR0078-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AR0078-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AR0078-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AZ0156-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AZ0156-C.json index 7b0a1936..4a9879fe 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AZ0156-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/AZ0156-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "AZ0156-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/BL0358-C.json b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/BL0358-C.json index ce655540..a8473db1 100644 --- a/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/BL0358-C.json +++ b/pipelines/short-read-alignment-and-genotyping-vector/gcp/input_files/validation/BL0358-C.json @@ -1,17 +1,17 @@ { "ShortReadAlignmentAndGenotyping.sample_id": "BL0358-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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-vector/gcp/input_files/AB0252-C.json b/pipelines/short-read-alignment-vector/gcp/input_files/AB0252-C.json index 3b54efbf..52036e87 100644 --- a/pipelines/short-read-alignment-vector/gcp/input_files/AB0252-C.json +++ b/pipelines/short-read-alignment-vector/gcp/input_files/AB0252-C.json @@ -1,16 +1,16 @@ { "ShortReadAlignment.sample_id": "AB0252-C", "ShortReadAlignment.output_basename": "AB0252-C", - "ShortReadAlignment.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/lanelets.tsv", + "ShortReadAlignment.input_file": "gs://malariagen/ShortReadAlignment/inputs/lanelets_remote_paths.tsv", "ShortReadAlignment.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" }, "ShortReadAlignment.runTimeSettings": { "preemptible_tries": 0, @@ -20,6 +20,8 @@ "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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-vector/gcp/input_files/AN0131-C.json b/pipelines/short-read-alignment-vector/gcp/input_files/AN0131-C.json index 0f76654a..10bc59e4 100644 --- a/pipelines/short-read-alignment-vector/gcp/input_files/AN0131-C.json +++ b/pipelines/short-read-alignment-vector/gcp/input_files/AN0131-C.json @@ -1,16 +1,16 @@ { "ShortReadAlignment.sample_id": "AN0131-C", "ShortReadAlignment.output_basename": "AN0131-C", - "ShortReadAlignment.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/lanelets.tsv", + "ShortReadAlignment.input_file": "gs://malariagen/ShortReadAlignment/inputs/lanelets_remote_paths.tsv", "ShortReadAlignment.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" }, "ShortReadAlignment.runTimeSettings": { "preemptible_tries": 0, @@ -20,6 +20,8 @@ "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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0079-C.json b/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0079-C.json index 9d6db7d7..e6508174 100644 --- a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0079-C.json +++ b/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0079-C.json @@ -1,16 +1,16 @@ { "ShortReadAlignment.sample_id": "AV0079-C", "ShortReadAlignment.output_basename": "AV0079-C", - "ShortReadAlignment.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/lanelets_no_crams.tsv", + "ShortReadAlignment.input_file": "gs://malariagen/ShortReadAlignment/inputs/lanelets_gs_paths.tsv", "ShortReadAlignment.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" }, "ShortReadAlignment.runTimeSettings": { "preemptible_tries": 0, @@ -20,6 +20,8 @@ "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" } } \ No newline at end of file diff --git a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C-fastqs.json b/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C-fastqs.json deleted file mode 100644 index 9b05a5c1..00000000 --- a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C-fastqs.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "ShortReadAlignment.sample_id": "AV0148-C", - "ShortReadAlignment.output_basename": "AV0148-C", - "ShortReadAlignment.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/AV0148-C_lanelets_fastqs_only.tsv", - "ShortReadAlignment.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" - }, - "ShortReadAlignment.runTimeSettings": { - "preemptible_tries": 0, - "gatk_docker": "broadinstitute/gatk3:3.7-0", - "picard_docker": "us.gcr.io/broad-gotc-prod/malariagen/picard:2.9.2", - "bwa_docker": "us.gcr.io/broad-gotc-prod/malariagen/bwa:0.7.15", - "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" - } -} \ No newline at end of file diff --git a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C.json b/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C.json index e5be5a91..a3a6a7fd 100644 --- a/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C.json +++ b/pipelines/short-read-alignment-vector/gcp/input_files/small/AV0148-C.json @@ -1,16 +1,16 @@ { "ShortReadAlignment.sample_id": "AV0148-C", "ShortReadAlignment.output_basename": "AV0148-C", - "ShortReadAlignment.input_file": "gs://broad-gotc-dev-storage/malariaGEN/ag1000g-phase1-minimal/lanelets_gs.tsv", + "ShortReadAlignment.input_file": "gs://malariagen/ShortReadAlignment/inputs/lanelets_gs_paths.tsv", "ShortReadAlignment.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" }, "ShortReadAlignment.runTimeSettings": { "preemptible_tries": 0, @@ -20,6 +20,8 @@ "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" } } \ No newline at end of file