From 1f776f47d4e9ab5c2d4ceba62c727adbff6260f9 Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Mon, 11 Mar 2024 17:15:12 -0700
Subject: [PATCH 1/4] fix: Use pyyaml SafeLoader to suppress deprecation
 warning.

---
 README.md                                         | 2 +-
 workflows/tertiary_analysis/tertiary_analysis.wdl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 3dc28bb3..a9da25c9 100644
--- a/README.md
+++ b/README.md
@@ -266,7 +266,7 @@ The Docker image used by a particular step of the workflow can be identified by
 | 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 1.13.1](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) |
+| 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/cec77c6042cc3c465d252d40c1ade89e3c58cf16/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) |
 | slivar | <ul><li>[slivar 0.2.2](https://github.com/brentp/slivar/releases/tag/v0.2.2)</li><li>[bcftools 1.14](https://github.com/samtools/bcftools/releases/tag/1.14)</li><li>[vcfpy 0.13.3](https://github.com/bihealth/vcfpy/releases/tag/v0.13.3)</li><li>[pysam 0.19.1](https://github.com/pysam-developers/pysam/releases/tag/v0.19.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/slivar) |
 | svpack | <ul><li>[svpack 36180ae6](https://github.com/PacificBiosciences/svpack/tree/a82598ebc4013bf32e70295b83b380ada6302c4a)</li><li>[htslib 1.18](https://github.com/samtools/htslib/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/8edbc516abc0ff43ac279b48018003923721b054/docker/svpack) |
diff --git a/workflows/tertiary_analysis/tertiary_analysis.wdl b/workflows/tertiary_analysis/tertiary_analysis.wdl
index 69776c37..d7efc1ec 100644
--- a/workflows/tertiary_analysis/tertiary_analysis.wdl
+++ b/workflows/tertiary_analysis/tertiary_analysis.wdl
@@ -133,7 +133,7 @@ task write_yaml_ped_phrank {
 	}
 
 	runtime {
-		docker: "~{runtime_attributes.container_registry}/pyyaml@sha256:af6f0689a7412b1edf76bd4bf6434e7fa6a86192eebf19573e8618880d9c1dbb"
+		docker: "~{runtime_attributes.container_registry}/pyyaml@sha256:8749239ba12a78d899f0dba4f55ddc260c42d4bfa60895bd11a628d4cfdef635"
 		cpu: 2
 		memory: "4 GB"
 		disk: disk_size + " GB"

From b5f8d0171856ca8a02336d797562973230c09c3d Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 12 Mar 2024 00:20:03 +0000
Subject: [PATCH 2/4] 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 179ef52d..c417354b 100644
--- a/wdl-ci.config.json
+++ b/wdl-ci.config.json
@@ -709,7 +709,7 @@
       "tasks": {
         "write_yaml_ped_phrank": {
           "key": "write_yaml_ped_phrank",
-          "digest": "e4yxyjj6vw35pxz434pgfalxpa4xh72n",
+          "digest": "4efgfhkb2mx3blda3i2qksjsqomcwqel",
           "tests": [
             {
               "inputs": {

From 759de6ab55a4711e8708fe7e5083f1db2d1e18d2 Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Mon, 11 Mar 2024 18:41:07 -0700
Subject: [PATCH 3/4] fix: Correct order of parents output by parse_cohort.py

---
 workflows/tertiary_analysis/tertiary_analysis.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/tertiary_analysis/tertiary_analysis.wdl b/workflows/tertiary_analysis/tertiary_analysis.wdl
index d7efc1ec..f782fb4d 100644
--- a/workflows/tertiary_analysis/tertiary_analysis.wdl
+++ b/workflows/tertiary_analysis/tertiary_analysis.wdl
@@ -133,7 +133,7 @@ task write_yaml_ped_phrank {
 	}
 
 	runtime {
-		docker: "~{runtime_attributes.container_registry}/pyyaml@sha256:8749239ba12a78d899f0dba4f55ddc260c42d4bfa60895bd11a628d4cfdef635"
+		docker: "~{runtime_attributes.container_registry}/pyyaml@sha256:f51db733249c29aec06fad2ab02695379aeebabb81fe30f36209d737dd381be1"
 		cpu: 2
 		memory: "4 GB"
 		disk: disk_size + " GB"

From b4a24e0a71cde471e6df2e2da9fcc01e9f19f7bb Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Mon, 11 Mar 2024 18:44:41 -0700
Subject: [PATCH 4/4] docs: Update docs for pyyaml.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a9da25c9..df01796f 100644
--- a/README.md
+++ b/README.md
@@ -266,7 +266,7 @@ The Docker image used by a particular step of the workflow can be identified by
 | 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 1.13.1](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/cec77c6042cc3c465d252d40c1ade89e3c58cf16/docker/pyyaml) |
+| 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/e421243d68aed4c7ed85bf90d6a82d738f292a28/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) |
 | slivar | <ul><li>[slivar 0.2.2](https://github.com/brentp/slivar/releases/tag/v0.2.2)</li><li>[bcftools 1.14](https://github.com/samtools/bcftools/releases/tag/1.14)</li><li>[vcfpy 0.13.3](https://github.com/bihealth/vcfpy/releases/tag/v0.13.3)</li><li>[pysam 0.19.1](https://github.com/pysam-developers/pysam/releases/tag/v0.19.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/slivar) |
 | svpack | <ul><li>[svpack 36180ae6](https://github.com/PacificBiosciences/svpack/tree/a82598ebc4013bf32e70295b83b380ada6302c4a)</li><li>[htslib 1.18](https://github.com/samtools/htslib/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/8edbc516abc0ff43ac279b48018003923721b054/docker/svpack) |