Merge branch 'develop' into feature/deepvariant-1.6

PacificBiosciences · Dec 9, 2023 · 58d1e46 · 58d1e46
2 parents dea1ebd + fd1b806
commit 58d1e46
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diff --git 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/94bbc94044ed8ee5dace9ebdc92756884535be93/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/wdl-ci.config.json b/wdl-ci.config.json
@@ -25,7 +25,7 @@
       "tasks": {
         "pbmm2_align": {
           "key": "pbmm2_align",
-          "digest": "3r4icze5zkps7m6xoruzvnfzk2fp4gqd",
+          "digest": "lo45v7z6rbh2uvh7nvnjf66udnoxfz2m",
           "tests": [
             {
               "inputs": {

diff --git 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:d92495f9a81d5d7edc8b394e4fa5f942027a37f9143ac4ab6cfeda1b7b320d2e"
 		cpu: threads
 		memory: mem_gb + " GB"
 		disk: disk_size + " GB"