broadinstitute · kevinpalis · Jun 26, 2023 · Jun 26, 2023 · Jun 26, 2023 · Jun 26, 2023
diff --git a/beta-pipelines/skylab/ATAC/ATAC.wdl b/beta-pipelines/skylab/ATAC/ATAC.wdl
@@ -241,7 +241,7 @@ task BWAPairedEndAlignment {
     read_group_sample_name: "the read group sample to be added upon alignment"
     cpu: "the number of cpu cores to use during alignment"
     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/pytools:1.0.0-1661263730)"
+    docker_image: "the docker image using BWA to be used (default: us.gcr.io/broad-gotc-prod/bwa:1.0.0-0.7.17-1660770463)"
   }
 
   # runtime requirements based upon input file size
@@ -673,21 +673,21 @@ task MakeCompliantBAM {
   input {
     File bam_input
     String output_base_name
-    String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+    String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
   }
 
   parameter_meta {
     bam_input: "the bam with barcodes in the read ids that need to be converted to barcodes in bam tags"
     output_base_name: "base name to be used for the output of the task"
-    docker_image: "the docker image using the python script to convert the bam barcodes/read ids (default: us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730)"
+    docker_image: "the docker image using the python script to convert the bam barcodes/read ids (default: us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671)"
   }
 
   Int disk_size = ceil(2.5 * (if size(bam_input, "GiB") < 1 then 1 else size(bam_input, "GiB")))
 
   String compliant_bam_output_name = output_base_name + ".compliant.bam"
 
   command {
-    /usr/gitc/makeCompliantBAM.py \
+    /warptools/scripts/makeCompliantBAM.py \
       --input-bam ~{bam_input} \
       --output-bam ~{compliant_bam_output_name}
   }
@@ -707,15 +707,15 @@ task MakeCompliantBAM {
 task BreakoutSnap {
     input {
         File snap_input
-        String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+        String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
         String bin_size_list
     }
     Int num_threads = 1
     Float input_size = size(snap_input, "GiB")
     command {
         set -euo pipefail
         mkdir output
-        /usr/gitc/breakoutSnap.py --input ~{snap_input} \
+        /warptools/scripts/breakoutSnap.py --input ~{snap_input} \
             --output-prefix output/
     }
     output {

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,8 +1,11 @@
 # 1.0.1
-2023-07-11 (Date of Last Commit)
 
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in StarAlign and updated command paths accordingly
 * Updated the CountAlignments task in the FeatureCounts.wdl to use a new docker image. This change does not affect the Multiome pipeline
 
+
 # 1.0.0
 2023-06-22 (Date of Last Commit)
 

diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,3 +1,7 @@
+# 5.8.4
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in StarAlign and updated command paths accordingly
 
 # 5.8.3
 2023-06-23 (Date of Last Commit)

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -67,7 +67,7 @@ workflow Optimus {
 
   # version of this pipeline
 
-  String pipeline_version = "5.8.3"
+  String pipeline_version = "5.8.4"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))

diff --git a/pipelines/skylab/scATAC/scATAC.changelog.md b/pipelines/skylab/scATAC/scATAC.changelog.md
@@ -1,3 +1,8 @@
+# 1.3.2
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools and updated command paths accordingly
+
 # 1.3.1
 2023-01-19 (Date of Last Commit)
 

diff --git a/pipelines/skylab/scATAC/scATAC.wdl b/pipelines/skylab/scATAC/scATAC.wdl
@@ -15,7 +15,7 @@ workflow scATAC {
         String bin_size_list = "10000"
     }
 
-    String pipeline_version = "1.3.1"
+    String pipeline_version = "1.3.2"
 
     parameter_meta {
         input_fastq1: "read 1 input fastq, the read names must be tagged with the cellular barcodes"
@@ -254,7 +254,7 @@ task MakeCompliantBAM {
     input {
         File input_bam
         String output_bam_filename
-        String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+        String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
         Int cpu = 1
         Int disk =  ceil(3 * (size(input_bam, "GiB"))) + 100
         Int machine_mem_mb = 4000
@@ -271,7 +271,7 @@ task MakeCompliantBAM {
     command {
         set -euo pipefail
 
-        /usr/gitc/makeCompliantBAM.py --input-bam ~{input_bam} --output-bam ~{output_bam_filename}
+        /warptools/scripts/makeCompliantBAM.py --input-bam ~{input_bam} --output-bam ~{output_bam_filename}
     }
 
     output {
@@ -291,7 +291,7 @@ task MakeCompliantBAM {
 task BreakoutSnap {
     input {
         File snap_input
-        String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+        String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
         String bin_size_list
         String input_id
         Int preemptible = 3
@@ -310,7 +310,7 @@ task BreakoutSnap {
     command {
         set -euo pipefail
         mkdir output
-        python3 /usr/gitc/breakoutSnap.py --input ~{snap_input} \
+        python3 /warptools/scripts/breakoutSnap.py --input ~{snap_input} \
             --output-prefix output/~{input_id}_
     }
 

diff --git a/pipelines/skylab/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.10
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in StarAlign and LoomUtils, and updated command paths accordingly
+
 # 1.0.9
 2023-06-14 (Date of Last Commit)
 

diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -23,7 +23,7 @@ import "../../../tasks/skylab/MergeSortBam.wdl" as Merge
 
 workflow SlideSeq {
 
-    String pipeline_version = "1.0.9"
+    String pipeline_version = "1.0.10"
 
     input {
         Array[File] r1_fastq

diff --git a/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md b/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md
@@ -1,3 +1,8 @@
+# 2.2.22
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in LoomUtils, and updated command paths accordingly
+
 # 2.2.21
 2023-04-19 (Date of Last Commit)
 

diff --git a/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl b/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl
@@ -40,7 +40,7 @@ workflow MultiSampleSmartSeq2 {
       Boolean paired_end
   }
   # Version of this pipeline
-  String pipeline_version = "2.2.21"
+  String pipeline_version = "2.2.22"
 
   if (false) {
      String? none = "None"

diff --git a/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,8 +1,10 @@
 # 1.2.25
 2023-07-11 (Date of Last Commit)
 
+* Changed Pytools container to Warp-tools in LoomUtils, and updated command paths accordingly
 * Updated the CountAlignments task in the FeatureCounts.wdl to use a new docker image. This change does not affect the MultiSampleSmartSeq2SingleNucleus pipeline
 
+
 # 1.2.24
 2023-06-23 (Date of Last Commit)
 

diff --git a/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md b/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 5.1.21
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in LoomUtils, and updated command paths accordingly
+
 # 5.1.20
 2023-04-19 (Date of Last Commit)
 

diff --git a/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl b/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl
@@ -36,7 +36,7 @@ workflow SmartSeq2SingleSample {
   }
 
   # version of this pipeline
-  String pipeline_version = "5.1.20"
+  String pipeline_version = "5.1.21"
 
   parameter_meta {
     genome_ref_fasta: "Genome reference in fasta format"

diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
@@ -401,7 +401,7 @@ task MergeStarOutput {
     String input_id
 
     #runtime values
-    String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
     Int machine_mem_mb = 8250
     Int cpu = 1
     Int disk = ceil(size(matrix, "Gi") * 2) + 10
@@ -426,7 +426,7 @@ task MergeStarOutput {
     declare -a matrix_files=(~{sep=' ' matrix})
 
    # create the  compressed raw count matrix with the counts, gene names and the barcodes
-    python3 /usr/gitc/create-merged-npz-output.py \
+    python3 /warptools/scripts/create-merged-npz-output.py \
         --barcodes ${barcodes_files[@]} \
         --features ${features_files[@]} \
         --matrix ${matrix_files[@]} \

diff --git a/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl b/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
@@ -13,12 +13,12 @@ task ValidateSmartSeq2Plate {
     # catch intermittent failures
     set -eo pipefail
 
-   python3 /usr/gitc/loomCompare.py --truth-loom ~{truth_loom} --check-loom ~{loom_output} --delta-cutoff 10
+   python3 /warptools/scripts/loomCompare.py --truth-loom ~{truth_loom} --check-loom ~{loom_output} --delta-cutoff 10
 
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+    docker: "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
     cpu: 1
     memory: "8 GiB"
     disks: "local-disk 1${disk_size} HDD"

diff --git a/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl b/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl
@@ -16,7 +16,7 @@ task ValidateSnSmartSeq2 {
     set -eo pipefail
 
     #compare looms
-    python3 /usr/gitc/loomCompare.py --truth-loom ~{truth_loom} --check-loom ~{loom_output} --delta-cutoff 10
+    python3 /warptools/scripts/loomCompare.py --truth-loom ~{truth_loom} --check-loom ~{loom_output} --delta-cutoff 10
 
     # calculate hashes; awk is used to extract the hash from the md5sum output that contains both
     # a hash and the filename that was passed. We parse the first 7 columns because a bug in RSEM
@@ -32,7 +32,7 @@ task ValidateSnSmartSeq2 {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
+    docker: "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
     cpu: 1
     memory: "8 GB"
     disks: "local-disk 1${disk_size} HDD"

diff --git a/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md b/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md
@@ -109,11 +109,11 @@ The SnapCellByBin task uses the Snap file to create cell-by-bin count matrices i
 
 #### MakeCompliantBAM
 
-The MakeCompliantBAM task uses a [custom python script (here)](https://github.com/broadinstitute/warp/blob/develop/dockers/skylab/pytools/tools/makeCompliantBAM.py) to make a GA4GH compliant BAM by moving the cellular barcodes in the read names to the CB tag.
+The MakeCompliantBAM task uses a [custom python script (here)](https://github.com/broadinstitute/warp-tools/blob/develop/tools/scripts/makeCompliantBAM.py) to make a GA4GH compliant BAM by moving the cellular barcodes in the read names to the CB tag.
 
 #### BreakoutSnap
 
-The BreakoutSnap task extracts data from the Snap file and exports it to individual CSVs. These CSV outputs are listed in the table in the Outputs section below. The code is available [here](https://github.com/broadinstitute/warp/tree/master/dockers/skylab/snap-breakout/breakoutSnap.py).
+The BreakoutSnap task extracts data from the Snap file and exports it to individual CSVs. These CSV outputs are listed in the table in the Outputs section below. The code is available [here](https://github.com/broadinstitute/warp-tools/blob/develop/tools/scripts/breakoutSnap.py).
 
 ## Outputs