tweak dt to make DOI, use dv gpu container

vgteam · Jun 17, 2022 · 1e77116 · 1e77116
1 parent 3e54e07
commit 1e77116
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Showing 4 changed files with 24 additions and 35 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -1,5 +1,20 @@
 version: 1.2
 workflows:
+ - name: GiraffeDeepTrio
+ subclass: WDL
+ description: Core VG Giraffe mapping and DeepTrio calling workflow for maternal-paternal-child sample datasets. It takes as inputs reads in FASTQ and graphs containing the population-based haplotypes to genotype. The graphs files required include the XG, GCSA, GBWT, graph GBWT, Distance and Minimizer indexes. It outputs a VCF file and BAM file for the child along with optional RTG and hap.py vcf evaluation if the user provides benchmark truth-set VCFs.
+ primaryDescriptorPath: /workflows/giraffe_and_deeptrio.wdl
+ testParameterFiles:
+ - /params/vg_hprc_deeptrio_map_call.inputs_tiny.gs_url.json
+ branches:
+ - master
+ authors:
+ - name: Charles Markello
+ email: cmarkell@ucsc.edu
+ - name: Jean Monlong
+ email: jmonlong@ucsc.edu
+ - name: Adam Novak
+ email: anovak@soe.ucsc.edu
  - name: GiraffeDeepVariant
  subclass: WDL
  description: Maps raw short reads from a pair of FASTQs or a CRAM file on a pangenome with vg Giraffe and call variants with DeepVariant.

diff --git a/workflows/giraffe_and_deeptrio.mapper.wdl b/workflows/giraffe_and_deeptrio.mapper.wdl
@@ -15,8 +15,6 @@ workflow vgGiraffeMap {
  File INPUT_READ_FILE_1 # Input sample 1st read pair fastq.gz
  File INPUT_READ_FILE_2 # Input sample 2nd read pair fastq.gz
  String SAMPLE_NAME # The sample name
- # VG Container used in the pipeline (e.g. quay.io/vgteam/vg:v1.16.0)
- String VG_CONTAINER = "quay.io/vgteam/vg:v1.36.0"
  Int READS_PER_CHUNK = 20000000 # Number of reads contained in each mapping chunk (20000000 for wgs)
  String? GIRAFFE_OPTIONS # (OPTIONAL) extra command line options for Giraffe mapper
  File PATH_LIST_FILE # Text file where each line is a path name in the XG index, to use instead of CONTIGS. If neither is given, paths are extracted from the XG and subset to chromosome-looking paths.
@@ -47,7 +45,6 @@ workflow vgGiraffeMap {
  input:
  in_read_file=INPUT_READ_FILE_1,
  in_pair_id="1",
- in_vg_container=VG_CONTAINER,
  in_reads_per_chunk=READS_PER_CHUNK,
  in_split_read_cores=SPLIT_READ_CORES,
  in_split_read_disk=SPLIT_READ_DISK
@@ -56,7 +53,6 @@ workflow vgGiraffeMap {
  input:
  in_read_file=INPUT_READ_FILE_2,
  in_pair_id="2",
- in_vg_container=VG_CONTAINER,
  in_reads_per_chunk=READS_PER_CHUNK,
  in_split_read_cores=SPLIT_READ_CORES,
  in_split_read_disk=SPLIT_READ_DISK
@@ -69,7 +65,6 @@ workflow vgGiraffeMap {
  input:
  in_xg_file=XG_FILE,
  in_path_list_file=PATH_LIST_FILE,
- in_vg_container=VG_CONTAINER,
  in_extract_disk=MAP_DISK,
  in_extract_mem=MAP_MEM
  }
@@ -96,7 +91,6 @@ workflow vgGiraffeMap {
  input:
  in_left_read_pair_chunk_file=read_pair_chunk_files.left,
  in_right_read_pair_chunk_file=read_pair_chunk_files.right,
- in_vg_container=VG_CONTAINER,
  in_giraffe_options=GIRAFFE_OPTIONS,
  in_xg_file=XG_FILE,
  in_gbwt_file=GBWT_FILE,
@@ -256,7 +250,6 @@ task splitReads {
  input {
  File in_read_file
  String in_pair_id
- String in_vg_container
  Int in_reads_per_chunk
  Int in_split_read_cores
  Int in_split_read_disk
@@ -293,7 +286,6 @@ task splitReads {
 task extractSubsetPathNames {
  input {
  File in_xg_file
- String in_vg_container
  Int in_extract_disk
  Int in_extract_mem
  }
@@ -314,15 +306,14 @@ task extractSubsetPathNames {
  preemptible: 2
  memory: in_extract_mem + " GB"
  disks: "local-disk " + in_extract_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
 task extractReference {
  input {
  File in_xg_file
  File in_path_list_file
- String in_vg_container
  Int in_extract_disk
  Int in_extract_mem
  }
@@ -344,7 +335,7 @@ task extractReference {
  preemptible: 2
  memory: in_extract_mem + " GB"
  disks: "local-disk " + in_extract_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
@@ -390,7 +381,6 @@ task runVGGIRAFFE {
  File in_dist_file
  File in_min_file
  File in_ref_dict
- String in_vg_container
  String? in_giraffe_options
  String in_sample_name
  Int in_map_cores
@@ -435,7 +425,7 @@ task runVGGIRAFFE {
  memory: in_map_mem + " GB"
  cpu: in_map_cores
  disks: "local-disk " + in_map_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
@@ -1060,7 +1050,6 @@ task bgzipMergedVCF {
  input {
  String in_sample_name
  File in_merged_vcf_file
- String in_vg_container
  Int in_call_disk
  Int in_call_mem
  }
@@ -1091,7 +1080,7 @@ task bgzipMergedVCF {
  time: 30
  memory: in_call_mem + " GB"
  disks: "local-disk " + in_call_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 

diff --git a/workflows/giraffe_and_deeptrio.wdl b/workflows/giraffe_and_deeptrio.wdl
@@ -23,8 +23,6 @@ workflow vgGiraffeDeeptrio {
  String SAMPLE_NAME # The child sample name
  String MATERNAL_NAME # The maternal sample name
  String PATERNAL_NAME # The paternal sample name
- # VG Container used in the pipeline (e.g. quay.io/vgteam/vg:v1.16.0)
- String VG_CONTAINER = "quay.io/vgteam/vg:v1.36.0"
  Int READS_PER_CHUNK = 20000000 # Number of reads contained in each mapping chunk (20000000 for wgs)
  String? GIRAFFE_OPTIONS # (OPTIONAL) extra command line options for Giraffe mapper
  Array[String]+? CONTIGS # (OPTIONAL) Desired reference genome contigs, which are all paths in the XG index.
@@ -77,7 +75,6 @@ workflow vgGiraffeDeeptrio {
  call extractSubsetPathNames {
  input:
  in_xg_file=XG_FILE,
- in_vg_container=VG_CONTAINER,
  in_extract_disk=MAP_DISK,
  in_extract_mem=MAP_MEM
  }
@@ -98,7 +95,6 @@ workflow vgGiraffeDeeptrio {
  input:
  in_xg_file=XG_FILE,
  in_path_list_file=pipeline_path_list_file,
- in_vg_container=VG_CONTAINER,
  in_extract_disk=MAP_DISK,
  in_extract_mem=MAP_MEM
  }
@@ -124,7 +120,6 @@ workflow vgGiraffeDeeptrio {
  INPUT_READ_FILE_1=MATERNAL_INPUT_READ_FILE_1,
  INPUT_READ_FILE_2=MATERNAL_INPUT_READ_FILE_2,
  SAMPLE_NAME=MATERNAL_NAME,
- VG_CONTAINER=VG_CONTAINER,
  READS_PER_CHUNK=READS_PER_CHUNK,
  GIRAFFE_OPTIONS=GIRAFFE_OPTIONS,
  PATH_LIST_FILE=pipeline_path_list_file,
@@ -154,7 +149,6 @@ workflow vgGiraffeDeeptrio {
  INPUT_READ_FILE_1=PATERNAL_INPUT_READ_FILE_1,
  INPUT_READ_FILE_2=PATERNAL_INPUT_READ_FILE_2,
  SAMPLE_NAME=PATERNAL_NAME,
- VG_CONTAINER=VG_CONTAINER,
  READS_PER_CHUNK=READS_PER_CHUNK,
  GIRAFFE_OPTIONS=GIRAFFE_OPTIONS,
  PATH_LIST_FILE=pipeline_path_list_file,
@@ -184,7 +178,6 @@ workflow vgGiraffeDeeptrio {
  INPUT_READ_FILE_1=CHILD_INPUT_READ_FILE_1,
  INPUT_READ_FILE_2=CHILD_INPUT_READ_FILE_2,
  SAMPLE_NAME=SAMPLE_NAME,
- VG_CONTAINER=VG_CONTAINER,
  READS_PER_CHUNK=READS_PER_CHUNK,
  GIRAFFE_OPTIONS=GIRAFFE_OPTIONS,
  PATH_LIST_FILE=pipeline_path_list_file,
@@ -411,7 +404,6 @@ workflow vgGiraffeDeeptrio {
  input:
  in_sample_name=SAMPLE_NAME,
  in_merged_vcf_file=concatVCFChunksChild.output_merged_vcf,
- in_vg_container=VG_CONTAINER,
  in_call_disk=CALL_DISK,
  in_call_mem=CALL_MEM
  }
@@ -431,7 +423,6 @@ workflow vgGiraffeDeeptrio {
  input:
  in_sample_name=MATERNAL_NAME,
  in_merged_vcf_file=concatVCFChunksMaternal.output_merged_vcf,
- in_vg_container=VG_CONTAINER,
  in_call_disk=CALL_DISK,
  in_call_mem=CALL_MEM
  }
@@ -451,7 +442,6 @@ workflow vgGiraffeDeeptrio {
  input:
  in_sample_name=PATERNAL_NAME,
  in_merged_vcf_file=concatVCFChunksPaternal.output_merged_vcf,
- in_vg_container=VG_CONTAINER,
  in_call_disk=CALL_DISK,
  in_call_mem=CALL_MEM
  }
@@ -509,7 +499,6 @@ task splitReads {
  input {
  File in_read_file
  String in_pair_id
- String in_vg_container
  Int in_reads_per_chunk
  Int in_split_read_cores
  Int in_split_read_disk
@@ -546,7 +535,6 @@ task splitReads {
 task extractSubsetPathNames {
  input {
  File in_xg_file
- String in_vg_container
  Int in_extract_disk
  Int in_extract_mem
  }
@@ -567,15 +555,14 @@ task extractSubsetPathNames {
  preemptible: 2
  memory: in_extract_mem + " GB"
  disks: "local-disk " + in_extract_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
 task extractReference {
  input {
  File in_xg_file
  File in_path_list_file
- String in_vg_container
  Int in_extract_disk
  Int in_extract_mem
  }
@@ -597,7 +584,7 @@ task extractReference {
  preemptible: 2
  memory: in_extract_mem + " GB"
  disks: "local-disk " + in_extract_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
@@ -643,7 +630,6 @@ task runVGGIRAFFE {
  File in_dist_file
  File in_min_file
  File in_ref_dict
- String in_vg_container
  String? in_giraffe_options
  String in_sample_name
  Int in_map_cores
@@ -688,7 +674,7 @@ task runVGGIRAFFE {
  memory: in_map_mem + " GB"
  cpu: in_map_cores
  disks: "local-disk " + in_map_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 
@@ -1313,7 +1299,6 @@ task bgzipMergedVCF {
  input {
  String in_sample_name
  File in_merged_vcf_file
- String in_vg_container
  Int in_call_disk
  Int in_call_mem
  }
@@ -1344,7 +1329,7 @@ task bgzipMergedVCF {
  time: 30
  memory: in_call_mem + " GB"
  disks: "local-disk " + in_call_disk + " SSD"
- docker: in_vg_container
+ docker: "quay.io/vgteam/vg:v1.38.0"
  }
 }
 

diff --git a/workflows/giraffe_and_deepvariant_lite.wdl b/workflows/giraffe_and_deepvariant_lite.wdl
@@ -975,7 +975,7 @@ task runDeepVariantCallVariants {
  gpuCount: 1
  nvidiaDriverVersion: "418.87.00"
  disks: "local-disk " + disk_size + " SSD"
- docker: "google/deepvariant:1.3.0"
+ docker: "google/deepvariant:1.3.0-gpu"
  }
 }