fix: Use pyyaml SafeLoader to suppress deprecation warning.

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/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) |

wdl-ci.config.json

@@ -709,7 +709,7 @@
       "tasks": {
         "write_yaml_ped_phrank": {
           "key": "write_yaml_ped_phrank",
-          "digest": "e4yxyjj6vw35pxz434pgfalxpa4xh72n",
+          "digest": "4efgfhkb2mx3blda3i2qksjsqomcwqel",
           "tests": [
             {
               "inputs": {

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:f51db733249c29aec06fad2ab02695379aeebabb81fe30f36209d737dd381be1"
 		cpu: 2
 		memory: "4 GB"
 		disk: disk_size + " GB"