Ph pd 2514 multiome on terra

pipelines/skylab/multiome/Multiome.changelog.md

@@ -1,3 +1,8 @@
+# 3.2.2
+2024-03-01 (Date of Last Commit)
+
+* Updated the Optimus.wdl to run on Azure. This change does not affect the Multiome pipeline.
+
 # 3.2.1
 2024-02-29 (Date of Last Commit)
 

pipelines/skylab/multiome/Multiome.wdl

@@ -4,12 +4,15 @@ import "../../../pipelines/skylab/multiome/atac.wdl" as atac
 import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/cellbender_remove_background.wdl" as CellBender
+import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Multiome {
-    String pipeline_version = "3.2.1"
+    String pipeline_version = "3.2.2"
 
     input {
+        String cloud_provider
         String input_id
+        String cloud_provider
 
         # Optimus Inputs
         String counting_mode = "sn_rna"
@@ -25,33 +28,56 @@ workflow Multiome {
         Boolean ignore_r1_read_length = false
         String star_strand_mode = "Forward"
         Boolean count_exons = false
-        File gex_whitelist = "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt"
         String? soloMultiMappers
 
         # ATAC inputs
         # Array of input fastq files
         Array[File] atac_r1_fastq
         Array[File] atac_r2_fastq
         Array[File] atac_r3_fastq
-
         # BWA tar reference
         File tar_bwa_reference
         # Chromosone sizes 
         File chrom_sizes
         # Trimadapters input
         String adapter_seq_read1 = "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG"
         String adapter_seq_read3 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG"
-        # Whitelist
-        File atac_whitelist = "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_atac.txt"
 
         # CellBender
         Boolean run_cellbender = false
 
     }
 
+    # Determine docker prefix based on cloud provider
+    String gcr_docker_prefix = "us.gcr.io/broad-gotc-prod/"
+    String acr_docker_prefix = "dsppipelinedev.azurecr.io/"
+    String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
+
+    # Define docker images
+    String snap_atac_docker_image = "snapatac2:1.0.5-2.3.2-1709230223"
+
+    # Define all whitelist files
+    File gcp_gex_whitelist = "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt"
+    File gcp_atac_whitelist = "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_atac.txt"
+    File azure_gex_whitelist = "https://datasetpublicbroadref.blob.core.windows.net/dataset/RNA/resources/arc-v1/737K-arc-v1_gex.txt"
+    File azure_atac_whitelist = "https://datasetpublicbroadref.blob.core.windows.net/dataset/RNA/resources/arc-v1/737K-arc-v1_atac.txt"
+
+    # Determine which whitelist files to use based on cloud provider
+    File gex_whitelist = if cloud_provider == "gcp" then gcp_gex_whitelist else azure_gex_whitelist
+    File atac_whitelist = if cloud_provider == "gcp" then gcp_atac_whitelist else azure_atac_whitelist
+
+    # Make sure either 'gcp' or 'azure' is supplied as cloud_provider input. If not, raise an error
+    if ((cloud_provider != "gcp") && (cloud_provider != "azure")) {
+        call utils.ErrorWithMessage as ErrorMessageIncorrectInput {
+            input:
+                message = "cloud_provider must be supplied with either 'gcp' or 'azure'."
+        }
+    }
+
     # Call the Optimus workflow
     call optimus.Optimus as Optimus {
         input:
+            cloud_provider = cloud_provider,
             counting_mode = counting_mode,
             r1_fastq = gex_r1_fastq,
             r2_fastq = gex_r2_fastq,
@@ -68,12 +94,14 @@ workflow Multiome {
             ignore_r1_read_length = ignore_r1_read_length,
             star_strand_mode = star_strand_mode,
             count_exons = count_exons,
-            soloMultiMappers = soloMultiMappers
+            soloMultiMappers = soloMultiMappers,
+            cloud_provider = cloud_provider
     }
 
     # Call the ATAC workflow
     call atac.ATAC as Atac {
         input:
+            cloud_provider = cloud_provider,
             read1_fastq_gzipped = atac_r1_fastq,
             read2_fastq_gzipped = atac_r2_fastq,
             read3_fastq_gzipped = atac_r3_fastq,
@@ -87,6 +115,7 @@ workflow Multiome {
     }
     call H5adUtils.JoinMultiomeBarcodes as JoinBarcodes {
         input:
+            docker_path = docker_prefix + snap_atac_docker_image,
             atac_h5ad = Atac.snap_metrics,
             gex_h5ad = Optimus.h5ad_output_file,
             gex_whitelist = gex_whitelist,
@@ -108,7 +137,6 @@ workflow Multiome {
                 hardware_preemptible_tries = 2,
                 hardware_zones = "us-central1-a us-central1-c",
                 nvidia_driver_version = "470.82.01"
-
         }
     }
 

pipelines/skylab/multiome/atac.changelog.md

@@ -1,4 +1,9 @@
-# 1.1.8
+# 1.1.9
+2024-03-01 (Date of Last Commit)
+
+*  Updated the Optimus.wdl to run on Azure. This change does not affect the ATAC pipeline.
+
+* # 1.1.8
 2024-02-07 (Date of Last Commit)
 
 * Updated the Metrics tasks to exclude mitochondrial genes from reads_mapped_uniquely, reads_mapped_multiple and reads_mapped_exonic, reads_mapped_exonic_as and reads_mapped_intergenic

pipelines/skylab/multiome/atac.json

@@ -4,6 +4,7 @@
   "ATAC.TrimAdapters.adapter_seq_read1": "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG",
   "ATAC.TrimAdapters.adapter_seq_read2": "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG",
   "ATAC.input_id": "scATAC",
+  "ATAC.cloud_provider":"gcp",
   "ATAC.tar_bwa_reference": "gs://fc-dd55e131-ef49-4d02-aa2a-20640daaae1e/submissions/8f0dd71a-b42f-4503-b839-3f146941758a/IndexRef/53a91851-1f6c-4ab9-af66-b338ffb28b5a/call-BwaMem2Index/GRCh38.primary_assembly.genome.bwamem2.fa.tar",
   "ATAC.preindex": "false"
 }

pipelines/skylab/multiome/atac.wdl

@@ -3,6 +3,7 @@ version 1.0
 import "../../../tasks/skylab/MergeSortBam.wdl" as Merge
 import "../../../tasks/skylab/FastqProcessing.wdl" as FastqProcessing
 import "../../../tasks/skylab/PairedTagUtils.wdl" as AddBB
+import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow ATAC {
   meta {
@@ -18,6 +19,7 @@ workflow ATAC {
 
     # Output prefix/base name for all intermediate files and pipeline outputs
     String input_id
+    String cloud_provider
 
     # Option for running files with preindex
     Boolean preindex = false
@@ -41,7 +43,27 @@ workflow ATAC {
     String adapter_seq_read3 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG"
   }
 
-  String pipeline_version = "1.1.8"
+  String pipeline_version = "1.1.9"
+
+  # Determine docker prefix based on cloud provider
+  String gcr_docker_prefix = "us.gcr.io/broad-gotc-prod/"
+  String acr_docker_prefix = "dsppipelinedev.azurecr.io/"
+  String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
+
+  # Docker image names
+  String warp_tools_2_0_0 = "warp-tools:2.0.0"
+  String cutadapt_docker = "cutadapt:1.0.0-4.4-1709146458"
+  String samtools_docker = "samtools-dist-bwa:3.0.0"
+  String upstools_docker = "upstools:1.0.0-2023.03.03-1704300311"
+  String snap_atac_docker = "snapatac2:1.0.4-2.3.1"
+
+  # Make sure either 'gcp' or 'azure' is supplied as cloud_provider input. If not, raise an error
+  if ((cloud_provider != "gcp") && (cloud_provider != "azure")) {
+    call utils.ErrorWithMessage as ErrorMessageIncorrectInput {
+        input:
+            message = "cloud_provider must be supplied with either 'gcp' or 'azure'."
+    }
+  }
 
   parameter_meta {
     read1_fastq_gzipped: "read 1 FASTQ file as input for the pipeline, contains read 1 of paired reads"
@@ -52,7 +74,6 @@ workflow ATAC {
     num_threads_bwa: "Number of threads for bwa-mem2 task (default: 128)"
     mem_size_bwa: "Memory size in GB for bwa-mem2 task (default: 512)"
     cpu_platform_bwa: "CPU platform for bwa-mem2 task (default: Intel Ice Lake)"
-
  }
 
   call GetNumSplits {
@@ -69,7 +90,8 @@ workflow ATAC {
       barcodes_fastq = read2_fastq_gzipped,
       output_base_name = input_id,
       num_output_files = GetNumSplits.ranks_per_node_out,
-      whitelist = whitelist
+      whitelist = whitelist,
+      docker_path = docker_prefix + warp_tools_2_0_0
   }
 
   scatter(idx in range(length(SplitFastq.fastq_R1_output_array))) {
@@ -79,7 +101,8 @@ workflow ATAC {
         read3_fastq = SplitFastq.fastq_R3_output_array[idx],
         output_base_name = input_id + "_" + idx,
         adapter_seq_read1 = adapter_seq_read1,
-        adapter_seq_read3 = adapter_seq_read3
+        adapter_seq_read3 = adapter_seq_read3,
+        docker_path = docker_prefix + cutadapt_docker
     }
   }
 
@@ -91,21 +114,24 @@ workflow ATAC {
         output_base_name = input_id,
         nthreads = num_threads_bwa, 
         mem_size = mem_size_bwa,
-        cpu_platform = cpu_platform_bwa
+        cpu_platform = cpu_platform_bwa,
+        docker_path = docker_prefix + samtools_docker
   }
 
   if (preindex) {
     call AddBB.AddBBTag as BBTag {
       input:
         bam = BWAPairedEndAlignment.bam_aligned_output,
-        input_id = input_id
+        input_id = input_id,
+        docker_path = docker_prefix + upstools_docker
     }
     call CreateFragmentFile as BB_fragment {
       input:
         bam = BBTag.bb_bam,
         chrom_sizes = chrom_sizes,
         annotations_gtf = annotations_gtf,
-        preindex = preindex
+        preindex = preindex,
+        docker_path = docker_prefix + snap_atac_docker
     }
   }
   if (!preindex) {
@@ -114,7 +140,8 @@ workflow ATAC {
         bam = BWAPairedEndAlignment.bam_aligned_output,
         chrom_sizes = chrom_sizes,
         annotations_gtf = annotations_gtf,
-        preindex = preindex
+        preindex = preindex,
+        docker_path = docker_prefix + snap_atac_docker
 
     }
   }
@@ -231,7 +258,7 @@ task TrimAdapters {
     # Runtime attributes/docker
     Int disk_size = ceil(2 * ( size(read1_fastq, "GiB") + size(read3_fastq, "GiB") )) + 200
     Int mem_size = 4
-    String docker_image = "us.gcr.io/broad-gotc-prod/cutadapt:1.0.0-4.4-1686752919"
+    String docker_path
   }
 
   parameter_meta {
@@ -242,7 +269,7 @@ task TrimAdapters {
     adapter_seq_read1: "cutadapt option for the sequence adapter for read 1 fastq"
     adapter_seq_read3: "cutadapt option for the sequence adapter for read 3 fastq"
     output_base_name: "base name to be used for the output of the task"
-    docker_image: "the docker image using cutadapt to be used (default:us.gcr.io/broad-gotc-prod/cutadapt:1.0.0-4.4-1686752919)"
+    docker_path: "The docker image path containing the runtime environment for this task"
     mem_size: "the size of memory used during trimming adapters"
     disk_size : "disk size used in trimming adapters step"
   }
@@ -269,7 +296,7 @@ task TrimAdapters {
 
   # use docker image for given tool cutadapat
   runtime {
-    docker: docker_image
+    docker: docker_path
     disks: "local-disk ${disk_size} HDD"
     memory: "${mem_size} GiB"
   }
@@ -290,7 +317,7 @@ task BWAPairedEndAlignment {
     String read_group_sample_name = "RGSN1"
     String suffix = "trimmed_adapters.fastq.gz"
     String output_base_name
-    String docker_image = "us.gcr.io/broad-gotc-prod/samtools-dist-bwa:2.0.0"
+    String docker_path
 
     # Runtime attributes
     Int disk_size = 2000
@@ -309,7 +336,7 @@ task BWAPairedEndAlignment {
     mem_size: "the size of memory used during alignment"
     disk_size : "disk size used in bwa alignment step"
     output_base_name: "basename to be used for the output of the task"
-    docker_image: "the docker image using BWA to be used (default: us.gcr.io/broad-gotc-prod/samtools-bwa-mem-2:1.0.0-2.2.1_x64-linux-1685469504)"
+    docker_path: "The docker image path containing the runtime environment for this task"
   }
 
   String bam_aligned_output_name = output_base_name + ".bam"
@@ -418,7 +445,7 @@ task BWAPairedEndAlignment {
   >>>
 
   runtime {
-    docker: docker_image
+    docker: docker_path
     disks: "local-disk ${disk_size} SSD"
     cpu: nthreads
     cpuPlatform: cpu_platform
@@ -442,6 +469,7 @@ task CreateFragmentFile {
     Int mem_size = 16
     Int nthreads = 1
     String cpuPlatform = "Intel Cascade Lake"
+    String docker_path
   }
 
   String bam_base_name = basename(bam, ".bam")
@@ -452,6 +480,7 @@ task CreateFragmentFile {
     chrom_sizes: "Text file containing chrom_sizes for genome build (i.e. hg38)."
     disk_size: "Disk size used in create fragment file step."
     mem_size: "The size of memory used in create fragment file."
+    docker_path: "The docker image path containing the runtime environment for this task"
   }
 
   command <<<
@@ -492,7 +521,7 @@ task CreateFragmentFile {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gotc-prod/snapatac2:1.0.4-2.3.1"
+    docker: docker_path
     disks: "local-disk ${disk_size} SSD"
     memory: "${mem_size} GiB"
     cpu: nthreads

pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json

@@ -1,6 +1,7 @@
 {
   "Multiome.annotations_gtf":"gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf",
   "Multiome.input_id":"10k_PBMC_downsampled",
+  "Multiome.cloud_provider":"gcp",
   "Multiome.gex_r1_fastq":[
     "gs://broad-gotc-test-storage/Multiome/input/plumbing/fastq_R1_gex.fastq.gz"
   ],
@@ -23,5 +24,6 @@
   "Multiome.Atac.cpu_platform_bwa":"Intel Cascade Lake",
   "Multiome.Atac.num_threads_bwa":"16",
   "Multiome.Atac.mem_size_bwa":"64", 
-  "Multiome.soloMultiMappers":"Uniform"
+  "Multiome.soloMultiMappers":"Uniform",
+  "Multiome.cloud_provider":"gcp"
 }

pipelines/skylab/multiome/test_inputs/Scientific/10k_pbmc.json

@@ -5,6 +5,7 @@
     "gs://broad-gotc-test-storage/Multiome/input/scientific/10k_PBMC_Multiome/10k_PBMC_Multiome_nextgem_Chromium_Controller_gex_S1_L002_I1_001.fastq.gz"
   ],
   "Multiome.input_id":"10k_PBMC",
+  "Multiome.cloud_provider":"gcp",
   "Multiome.gex_r1_fastq":[
     "gs://broad-gotc-test-storage/Multiome/input/scientific/10k_PBMC_Multiome/10k_PBMC_Multiome_nextgem_Chromium_Controller_gex_S1_L001_R1_001.fastq.gz",
     "gs://broad-gotc-test-storage/Multiome/input/scientific/10k_PBMC_Multiome/10k_PBMC_Multiome_nextgem_Chromium_Controller_gex_S1_L002_R1_001.fastq.gz"

pipelines/skylab/optimus/Optimus.changelog.md

@@ -1,3 +1,8 @@
+# 6.4.2
+2024-03-01 (Date of Last Commit)
+* Updated the Optimus.wdl to run on Azure.
+
+
 # 6.4.1
 2024-02-29 (Date of Last Commit)
 * Added mem and disk to inputs of Join Barcodes task of Multiome workflow; does not impact the Optimus workflow