From f2181196bf373dd1ccc757870b01163c934ca3bc Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Thu, 14 Dec 2023 15:24:06 -0800
Subject: [PATCH 1/2] feat: Update pbmm2 to 1.13.1

New container also has updated pysam script with silenced errors.
---
 README.md                                     | 2 +-
 workflows/sample_analysis/sample_analysis.wdl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 457449bb..4e5b694f 100644
--- a/README.md
+++ b/README.md
@@ -264,7 +264,7 @@ The Docker image used by a particular step of the workflow can be identified by
 | mosdepth | <ul><li>[mosdepth 0.2.9](https://github.com/brentp/mosdepth/releases/tag/v0.2.9)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/mosdepth) |
 | paraphase | <ul><li>[minimap2 2.17](https://github.com/lh3/minimap2/releases/tag/v2.17)</li><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li><li>[paraphase 2.2.3](https://github.com/PacificBiosciences/paraphase/releases/tag/v2.2.3)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/paraphase) |
 | pb-cpg-tools | <ul><li>[pb-CpG-tools v2.3.2](https://github.com/PacificBiosciences/pb-CpG-tools/releases/tag/v2.3.2)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/7481837d3b0f539adf4f64209a65cf28eebf3dba/docker/pb-cpg-tools) |
-| pbmm2 | <ul><li>[pbmm2 1.10.0](https://github.com/PacificBiosciences/pbmm2/releases/tag/v1.10.0)</li><li>[datamash 1.1.0](https://ftp.gnu.org/gnu/datamash/)</li><li>[pysam 0.16.0.1](https://github.com/pysam-developers/pysam/releases/tag/v0.16.0.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/pbmm2) |
+| pbmm2 | <ul><li>[pbmm2 1.13.1](https://github.com/PacificBiosciences/pbmm2/releases/tag/v1.13.1)</li><li>[datamash 1.1.0](https://ftp.gnu.org/gnu/datamash/)</li><li>[pysam 0.16.0.1](https://github.com/pysam-developers/pysam/releases/tag/v0.16.0.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6d3d818dce6f97454ac29f4ed96637e450a19f63/docker/pbmm2) |
 | pbsv | <ul><li>[pbsv 2.9.0](https://github.com/PacificBiosciences/pbsv/releases/tag/v2.9.0)</li><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/f9e33a757e6d8cb15696ac930a2efd0fd7a885d8/docker/pbsv) |
 | pyyaml | <ul><li>[pyyaml 5.3.1](https://github.com/yaml/pyyaml/releases/tag/5.3.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/f72e862bca2f209b9909e6043ef0197975762f27/docker/pyyaml) |
 | samtools | <ul><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/samtools) |
diff --git a/workflows/sample_analysis/sample_analysis.wdl b/workflows/sample_analysis/sample_analysis.wdl
index 1f4f1a8d..77e6196c 100644
--- a/workflows/sample_analysis/sample_analysis.wdl
+++ b/workflows/sample_analysis/sample_analysis.wdl
@@ -317,7 +317,7 @@ task pbmm2_align {
 	}
 
 	runtime {
-		docker: "~{runtime_attributes.container_registry}/pbmm2@sha256:1013aa0fd5fb42c607d78bfe3ec3d19e7781ad3aa337bf84d144c61ed7d51fa1"
+		docker: "~{runtime_attributes.container_registry}/pbmm2@sha256:ed9dcb4db98c81967fff15f50fca89c8495b1f270eee00e9bec92f46d14d7e2f"
 		cpu: threads
 		memory: mem_gb + " GB"
 		disk: disk_size + " GB"

From 511021e5f1cc8938646e52dd17a3b8af11464fe9 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 15 Dec 2023 00:17:48 +0000
Subject: [PATCH 2/2] update wdl-ci config file after successful tests

---
 wdl-ci.config.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wdl-ci.config.json b/wdl-ci.config.json
index 744d869f..a673b508 100644
--- a/wdl-ci.config.json
+++ b/wdl-ci.config.json
@@ -25,7 +25,7 @@
       "tasks": {
         "pbmm2_align": {
           "key": "pbmm2_align",
-          "digest": "3r4icze5zkps7m6xoruzvnfzk2fp4gqd",
+          "digest": "ntqgonovwrgxezaewjfw7oec4t34yvhp",
           "tests": [
             {
               "inputs": {