From e70e30c40d4f4e24d05b1c494ae0108a623800eb Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Mon, 26 Jun 2023 10:59:28 -0400
Subject: [PATCH 1/7] Changing pytools container usage to warp-tools

---
 beta-pipelines/skylab/ATAC/ATAC.wdl                       | 8 ++++----
 pipelines/skylab/scATAC/scATAC.wdl                        | 4 ++--
 tasks/skylab/LoomUtils.wdl                                | 6 +++---
 tasks/skylab/StarAlign.wdl                                | 2 +-
 .../pr/ValidateMultiSampleSmartSeq2.wdl                   | 2 +-
 .../pr/ValidateSmartSeq2SingleNucleus.wdl                 | 2 +-
 6 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/beta-pipelines/skylab/ATAC/ATAC.wdl b/beta-pipelines/skylab/ATAC/ATAC.wdl
index 6dfaedb83..b25b13008 100644
--- 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/warp-tools:1.0.1-1686932671)"
   }
 
   # runtime requirements based upon input file size
@@ -673,13 +673,13 @@ 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")))
@@ -707,7 +707,7 @@ 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
     }
     Int num_threads = 1
diff --git a/pipelines/skylab/scATAC/scATAC.wdl b/pipelines/skylab/scATAC/scATAC.wdl
index 3399afabb..4ebff22a5 100644
--- a/pipelines/skylab/scATAC/scATAC.wdl
+++ b/pipelines/skylab/scATAC/scATAC.wdl
@@ -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
@@ -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
diff --git a/tasks/skylab/LoomUtils.wdl b/tasks/skylab/LoomUtils.wdl
index 145b2ebc7..3db9b9cfe 100644
--- a/tasks/skylab/LoomUtils.wdl
+++ b/tasks/skylab/LoomUtils.wdl
@@ -3,7 +3,7 @@ version 1.0
 task SmartSeq2LoomOutput {
   input {
     #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"
     # the gene count file "<input_id>_rsem.genes.results" in the task results folder call-RSEMExpression
     File rsem_gene_results
     # file named "<input_id>_QCs.csv" in the folder  "call-GroupQCOutputs/glob-*" of the the SS2  output
@@ -169,7 +169,7 @@ task AggregateSmartSeq2Loom {
         String? species
         String? organ
         String pipeline_version
-        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 disk = 200
         Int machine_mem_mb = 4000
         Int cpu = 1
@@ -300,7 +300,7 @@ task SingleNucleusOptimusLoomOutput {
 task SingleNucleusSmartSeq2LoomOutput {
     input {
         #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"
 
         Array[File] alignment_summary_metrics
         Array[File] dedup_metrics
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index c3a59df19..8a5664323 100644
--- 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
diff --git a/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl b/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
index cdfbbeb4e..fcfb3b8ba 100644
--- a/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
+++ b/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
@@ -18,7 +18,7 @@ task ValidateSmartSeq2Plate {
   >>>
   
   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
index 80880c2b3..63464b367 100644
--- a/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl
+++ b/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl
@@ -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"

From 665b85fa8c2c8d9ff85a3f50283ea596cb59a31d Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Mon, 26 Jun 2023 11:08:00 -0400
Subject: [PATCH 2/7] Changing path to scripts accordingly

---
 beta-pipelines/skylab/ATAC/ATAC.wdl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/beta-pipelines/skylab/ATAC/ATAC.wdl b/beta-pipelines/skylab/ATAC/ATAC.wdl
index b25b13008..2210f0772 100644
--- 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/warp-tools:1.0.1-1686932671)"
+    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
@@ -687,7 +687,7 @@ task MakeCompliantBAM {
   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}
   }
@@ -715,7 +715,7 @@ task BreakoutSnap {
     command {
         set -euo pipefail
         mkdir output
-        /usr/gitc/breakoutSnap.py --input ~{snap_input} \
+        /warptools/scripts/breakoutSnap.py --input ~{snap_input} \
             --output-prefix output/
     }
     output {

From e95ba1b41fe979ebccc7b86d64b700f295aa26f0 Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Mon, 26 Jun 2023 14:50:04 -0400
Subject: [PATCH 3/7] Changing paths to scripts accordingly

---
 pipelines/skylab/scATAC/scATAC.wdl                        | 4 ++--
 tasks/skylab/LoomUtils.wdl                                | 8 ++++----
 tasks/skylab/StarAlign.wdl                                | 2 +-
 .../pr/ValidateMultiSampleSmartSeq2.wdl                   | 2 +-
 .../pr/ValidateSmartSeq2SingleNucleus.wdl                 | 2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/pipelines/skylab/scATAC/scATAC.wdl b/pipelines/skylab/scATAC/scATAC.wdl
index 4ebff22a5..327bf1c4e 100644
--- a/pipelines/skylab/scATAC/scATAC.wdl
+++ b/pipelines/skylab/scATAC/scATAC.wdl
@@ -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 {
@@ -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/tasks/skylab/LoomUtils.wdl b/tasks/skylab/LoomUtils.wdl
index 3db9b9cfe..ea0fdf895 100644
--- a/tasks/skylab/LoomUtils.wdl
+++ b/tasks/skylab/LoomUtils.wdl
@@ -32,7 +32,7 @@ task SmartSeq2LoomOutput {
   command {
     set -euo pipefail
 
-    python3 /usr/gitc/create_loom_ss2.py \
+    python3 /warptools/scripts/create_loom_ss2.py \
        --qc_files ~{sep=' ' smartseq_qc_files} \
        --rsem_genes_results  ~{rsem_gene_results} \
        --output_loom_path  "~{input_id}.loom" \
@@ -183,7 +183,7 @@ task AggregateSmartSeq2Loom {
       set -e
       
       # Merge the loom files
-      python3 /usr/gitc/ss2_loom_merge.py \
+      python3 /warptools/scripts/ss2_loom_merge.py \
       --input-loom-files ~{sep=' ' loom_input} \
       --output-loom-file "~{batch_id}.loom" \
       --batch_id ~{batch_id} \
@@ -347,7 +347,7 @@ task SingleNucleusSmartSeq2LoomOutput {
         do
         # creates a table with gene_id, gene_name, intron and exon counts
         echo "Running create_snss2_counts_csv."
-        python /usr/gitc/create_snss2_counts_csv.py \
+        python /warptools/scripts/create_snss2_counts_csv.py \
         --in-gtf ~{annotation_introns_added_gtf} \
         --intron-counts ${introns_counts_files[$i]} \
         --exon-counts ${exons_counts_files[$i]}  \
@@ -362,7 +362,7 @@ task SingleNucleusSmartSeq2LoomOutput {
 
         # create the loom file
         echo "Running create_loom_snss2."
-        python3 /usr/gitc/create_loom_snss2.py \
+        python3 /warptools/scripts/create_loom_snss2.py \
         --qc_files "${output_prefix[$i]}.Picard_group.csv" \
         --count_results  "${output_prefix[$i]}.exon_intron_counts.tsv" \
         --output_loom_path "${output_prefix[$i]}.loom" \
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 8a5664323..aa46396b6 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -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
index fcfb3b8ba..e66a54a29 100644
--- a/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
+++ b/tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
@@ -13,7 +13,7 @@ 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
 
   >>>
   
diff --git a/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl b/tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl
index 63464b367..4f43b068d 100644
--- 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

From be4f15c8794cb56c81b6ec1c5fa07f7e52949554 Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Tue, 27 Jun 2023 10:47:46 -0400
Subject: [PATCH 4/7] Updating scatac documentation

---
 pipelines/skylab/scATAC/scATAC.wdl                            | 2 +-
 .../docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pipelines/skylab/scATAC/scATAC.wdl b/pipelines/skylab/scATAC/scATAC.wdl
index 327bf1c4e..08dd19bca 100644
--- a/pipelines/skylab/scATAC/scATAC.wdl
+++ b/pipelines/skylab/scATAC/scATAC.wdl
@@ -271,7 +271,7 @@ task MakeCompliantBAM {
     command {
         set -euo pipefail
 
-        /warptools/scripts//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 {
diff --git a/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md b/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md
index 73d713b8a..cbe516076 100644
--- a/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md
+++ b/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md
@@ -108,11 +108,11 @@ 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
 

From 6c0f3bb6601488e72aa03ddd2824ab1e9f0c7ea9 Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Fri, 7 Jul 2023 09:57:44 -0400
Subject: [PATCH 5/7] Adding changelog update

---
 pipelines/skylab/scATAC/scATAC.changelog.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pipelines/skylab/scATAC/scATAC.changelog.md b/pipelines/skylab/scATAC/scATAC.changelog.md
index c9ad71222..8b7e6ff91 100644
--- 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)
 

From c89b6bfe93eee9af6572a49e804cdae9fe2c05cf Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Fri, 7 Jul 2023 10:57:45 -0400
Subject: [PATCH 6/7] Updated changelogs and pipeline version numbers.

---
 pipelines/skylab/multiome/Multiome.changelog.md              | 5 +++++
 pipelines/skylab/multiome/Multiome.wdl                       | 2 +-
 pipelines/skylab/optimus/Optimus.changelog.md                | 4 ++++
 pipelines/skylab/optimus/Optimus.wdl                         | 2 +-
 pipelines/skylab/scATAC/scATAC.wdl                           | 2 +-
 pipelines/skylab/slideseq/SlideSeq.changelog.md              | 5 +++++
 pipelines/skylab/slideseq/SlideSeq.wdl                       | 2 +-
 .../smartseq2_multisample/MultiSampleSmartSeq2.changelog.md  | 5 +++++
 .../skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl    | 2 +-
 .../MultiSampleSmartSeq2SingleNucleus.changelog.md           | 5 +++++
 .../MultiSampleSmartSeq2SingleNucleus.wdl                    | 2 +-
 .../SmartSeq2SingleSample.changelog.md                       | 5 +++++
 .../skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl | 2 +-
 13 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
index 8a6926bab..1f05e5317 100644
--- a/pipelines/skylab/multiome/Multiome.changelog.md
+++ b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.1
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in StarAlign and updated command paths accordingly
+
 # 1.0.0
 2023-06-22 (Date of Last Commit)
 
diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index dc1ad08d1..210a1ea07 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -4,7 +4,7 @@ import "../../../pipelines/skylab/multiome/atac.wdl" as atac
 import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 
 workflow Multiome {
-    String pipeline_version = "1.0.0"
+    String pipeline_version = "1.0.1"
 
     input {
         String input_id
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
index 216d14cfe..480504d21 100644
--- 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
index e6b41fe69..5801bd936 100644
--- 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.wdl b/pipelines/skylab/scATAC/scATAC.wdl
index 08dd19bca..10f456fc3 100644
--- 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"
diff --git a/pipelines/skylab/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
index 2252c8f60..bcb9e3c85 100644
--- 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
index ec631d8d2..5328906c2 100644
--- 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
index 5bc4212b9..64eb8bc7f 100644
--- 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
index 91c9d4f88..0717f23b7 100644
--- 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/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
index 61c9d639a..af7b13342 100644
--- a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
+++ b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.25
+2023-07-07 (Date of Last Commit)
+
+* Changed Pytools container to Warp-tools in LoomUtils, and updated command paths accordingly
+
 # 1.2.24
 2023-06-23 (Date of Last Commit)
 
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
index b595742c1..a2d85c804 100644
--- a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
+++ b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -40,7 +40,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
       String? input_id_metadata_field
   }
   # Version of this pipeline
-  String pipeline_version = "1.2.24"
+  String pipeline_version = "1.2.25"
 
   if (false) {
      String? none = "None"
diff --git a/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md b/pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md
index 421964d45..eb0432276 100644
--- 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
index efec1c416..b9df38485 100644
--- 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"

From a3bbe25d511eef286ebe9131da7ca28749edd511 Mon Sep 17 00:00:00 2001
From: Kevin Palis <palis@broadinstitute.org>
Date: Fri, 14 Jul 2023 16:16:22 -0400
Subject: [PATCH 7/7] Reverting LoomUtils to use pytools again because of some
 legacy libraries that just won't work with a more recent python container

---
 tasks/skylab/LoomUtils.wdl | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tasks/skylab/LoomUtils.wdl b/tasks/skylab/LoomUtils.wdl
index ea0fdf895..145b2ebc7 100644
--- a/tasks/skylab/LoomUtils.wdl
+++ b/tasks/skylab/LoomUtils.wdl
@@ -3,7 +3,7 @@ version 1.0
 task SmartSeq2LoomOutput {
   input {
     #runtime values
-    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
+    String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
     # the gene count file "<input_id>_rsem.genes.results" in the task results folder call-RSEMExpression
     File rsem_gene_results
     # file named "<input_id>_QCs.csv" in the folder  "call-GroupQCOutputs/glob-*" of the the SS2  output
@@ -32,7 +32,7 @@ task SmartSeq2LoomOutput {
   command {
     set -euo pipefail
 
-    python3 /warptools/scripts/create_loom_ss2.py \
+    python3 /usr/gitc/create_loom_ss2.py \
        --qc_files ~{sep=' ' smartseq_qc_files} \
        --rsem_genes_results  ~{rsem_gene_results} \
        --output_loom_path  "~{input_id}.loom" \
@@ -169,7 +169,7 @@ task AggregateSmartSeq2Loom {
         String? species
         String? organ
         String pipeline_version
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
+        String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
         Int disk = 200
         Int machine_mem_mb = 4000
         Int cpu = 1
@@ -183,7 +183,7 @@ task AggregateSmartSeq2Loom {
       set -e
       
       # Merge the loom files
-      python3 /warptools/scripts/ss2_loom_merge.py \
+      python3 /usr/gitc/ss2_loom_merge.py \
       --input-loom-files ~{sep=' ' loom_input} \
       --output-loom-file "~{batch_id}.loom" \
       --batch_id ~{batch_id} \
@@ -300,7 +300,7 @@ task SingleNucleusOptimusLoomOutput {
 task SingleNucleusSmartSeq2LoomOutput {
     input {
         #runtime values
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
+        String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
 
         Array[File] alignment_summary_metrics
         Array[File] dedup_metrics
@@ -347,7 +347,7 @@ task SingleNucleusSmartSeq2LoomOutput {
         do
         # creates a table with gene_id, gene_name, intron and exon counts
         echo "Running create_snss2_counts_csv."
-        python /warptools/scripts/create_snss2_counts_csv.py \
+        python /usr/gitc/create_snss2_counts_csv.py \
         --in-gtf ~{annotation_introns_added_gtf} \
         --intron-counts ${introns_counts_files[$i]} \
         --exon-counts ${exons_counts_files[$i]}  \
@@ -362,7 +362,7 @@ task SingleNucleusSmartSeq2LoomOutput {
 
         # create the loom file
         echo "Running create_loom_snss2."
-        python3 /warptools/scripts/create_loom_snss2.py \
+        python3 /usr/gitc/create_loom_snss2.py \
         --qc_files "${output_prefix[$i]}.Picard_group.csv" \
         --count_results  "${output_prefix[$i]}.exon_intron_counts.tsv" \
         --output_loom_path "${output_prefix[$i]}.loom" \