feat: Update pbmm2 to 1.13.1

New container also has updated pysam script with silenced errors.

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) |

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"