From 90144525b541e914870bb41a0e5734ad92ec2093 Mon Sep 17 00:00:00 2001
From: aawdeh <awdeh@broadinstitute.org>
Date: Fri, 2 Feb 2024 10:01:31 -0500
Subject: [PATCH] Change machine type and number of output files for
 fastqprocess optimus

---
 tasks/skylab/FastqProcessing.wdl |  2 +-
 tasks/skylab/StarAlign.wdl       | 86 ++++++++++----------------------
 2 files changed, 28 insertions(+), 60 deletions(-)

diff --git a/tasks/skylab/FastqProcessing.wdl b/tasks/skylab/FastqProcessing.wdl
index ac22cc38aa..7adbfef0a0 100644
--- a/tasks/skylab/FastqProcessing.wdl
+++ b/tasks/skylab/FastqProcessing.wdl
@@ -102,7 +102,7 @@ task FastqProcessing {
     fi
 
     fastqprocess \
-        --bam-size 30.0 \
+        --num-output-files 1 \
         --sample-id "~{sample_id}" \
         $FASTQS \
         --white-list "~{whitelist}" \
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 8ab0c8d615..b61030f56c 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -227,12 +227,15 @@ task STARsoloFastq {
 
     # runtime values
     String docker = "us.gcr.io/broad-gotc-prod/star:1.0.1-2.7.11a-1692706072"
-    Int machine_mem_mb = 64000
-    Int cpu = 8
+
+    String cpu_platform = "Intel Ice Lake"
+    Int machine_mem_mb = 512000
+    Int cpu = 128
+    Int disk = 2000
     # multiply input size by 2.2 to account for output bam file + 20% overhead, add size of reference.
-    Int disk = ceil((size(tar_star_reference, "Gi") * 3)) + ceil(size(r1_fastq, "Gi") * 20) +  ceil(size(r2_fastq, "Gi") * 20)
+    # Int disk = ceil((size(tar_star_reference, "Gi") * 3)) + ceil(size(r1_fastq, "Gi") * 20) +  ceil(size(r2_fastq, "Gi") * 20)
     # by default request non preemptible machine to make sure the slow star alignment step completes
-    Int preemptible = 3
+    Int preemptible = 1
   }
 
   meta {
@@ -292,7 +295,23 @@ task STARsoloFastq {
         ## single cell or whole cell
         COUNTING_MODE="Gene"
         echo "Running in ~{counting_mode} mode. The Star parameter --soloFeatures will be set to $COUNTING_MODE"
-        STAR \
+    elif [[ "~{counting_mode}" == "sn_rna" ]]
+    then
+        ## single nuclei
+        if [[ ~{count_exons} == false ]]
+        then
+            COUNTING_MODE="GeneFull_Ex50pAS"
+            echo "Running in ~{counting_mode} mode. Count_exons is false and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
+        else
+            COUNTING_MODE="GeneFull_Ex50pAS Gene"
+            echo "Running in ~{counting_mode} mode. Count_exons is true and the Star parameter --soloFeatures will be set to $COUNTING_MODE"     
+        fi
+    else
+        echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna.
+        exit 1;
+    fi
+
+    STAR \
         --soloType Droplet \
         --soloStrand ~{star_strand_mode} \
         --runThreadN ~{cpu} \
@@ -311,62 +330,10 @@ task STARsoloFastq {
         --soloBarcodeReadLength 0 \
         --soloCellReadStats Standard \
         ~{"--soloMultiMappers " + soloMultiMappers}
-    elif [[ "~{counting_mode}" == "sn_rna" ]]
-    then
-        ## single nuclei
-        if [[ ~{count_exons} == false ]]
-        then
-            COUNTING_MODE="GeneFull_Ex50pAS"
-            echo "Running in ~{counting_mode} mode. Count_exons is false and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
-            STAR \
-            --soloType Droplet \
-            --soloStrand ~{star_strand_mode} \
-            --runThreadN ~{cpu} \
-            --genomeDir genome_reference \
-            --readFilesIn "~{sep=',' r2_fastq}" "~{sep=',' r1_fastq}" \
-            --readFilesCommand "gunzip -c" \
-            --soloCBwhitelist ~{white_list} \
-            --soloUMIlen $UMILen --soloCBlen $CBLen \
-            --soloFeatures $COUNTING_MODE  \
-            --clipAdapterType CellRanger4 \
-            --outFilterScoreMin 30  \
-            --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
-            --soloUMIdedup 1MM_Directional_UMItools \
-            --outSAMtype BAM SortedByCoordinate \
-            --outSAMattributes UB UR UY CR CB CY NH GX GN sF \
-            --soloBarcodeReadLength 0 \
-            --soloCellReadStats Standard \
-            ~{"--soloMultiMappers " + soloMultiMappers}
-        else
-            COUNTING_MODE="GeneFull_Ex50pAS Gene"
-            echo "Running in ~{counting_mode} mode. Count_exons is true and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
-            STAR \
-            --soloType Droplet \
-            --soloStrand ~{star_strand_mode} \
-            --runThreadN ~{cpu} \
-            --genomeDir genome_reference \
-            --readFilesIn "~{sep=',' r2_fastq}" "~{sep=',' r1_fastq}" \
-            --readFilesCommand "gunzip -c" \
-            --soloCBwhitelist ~{white_list} \
-            --soloUMIlen $UMILen --soloCBlen $CBLen \
-            --soloFeatures $COUNTING_MODE \
-            --clipAdapterType CellRanger4 \
-            --outFilterScoreMin 30  \
-            --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
-            --soloUMIdedup 1MM_Directional_UMItools \
-            --outSAMtype BAM SortedByCoordinate \
-            --outSAMattributes UB UR UY CR CB CY NH GX GN sF \
-            --soloBarcodeReadLength 0 \
-            --soloCellReadStats Standard \
-            ~{"--soloMultiMappers " + soloMultiMappers}
-        fi
-    else
-        echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna.
-        exit 1;
-    fi
 
     echo "UMI LEN " $UMILen
 
+    # why is this here?
     touch barcodes_sn_rna.tsv
     touch features_sn_rna.tsv
     touch matrix_sn_rna.mtx
@@ -434,10 +401,11 @@ task STARsoloFastq {
   runtime {
     docker: docker
     memory: "~{machine_mem_mb} MiB"
-    disks: "local-disk ~{disk} HDD"
+    disks: "local-disk ~{disk} SSD"
     disk: disk + " GB" # TES
     cpu: cpu
     preemptible: preemptible
+    cpuPlatform: cpu_platform
   }
 
   output {