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feat: Update TRGT to 0.7.0 #101

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merged 2 commits into from
Dec 15, 2023
Merged

feat: Update TRGT to 0.7.0 #101

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200efc3
feat: Update TRGT to 0.7.0
williamrowell Dec 14, 2023
546990c
update wdl-ci config file after successful tests
github-actions[bot] Dec 14, 2023
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -270,7 +270,7 @@ The Docker image used by a particular step of the workflow can be identified by
| 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) |
| trgt | <ul><li>[trgt 0.5.0](https://github.com/PacificBiosciences/trgt/releases/tag/v0.5.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/d2a45e0213ac3fa631a51a48757c442d3ed550b6/docker/trgt) |
| trgt | <ul><li>[trgt 0.7.0](https://github.com/PacificBiosciences/trgt/releases/tag/v0.7.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/9aae7d50a4beb08a1869dd3ce1a0567ee4e5cbc2/docker/trgt) |

---

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4 changes: 2 additions & 2 deletions wdl-ci.config.json
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Expand Up @@ -142,7 +142,7 @@
},
"trgt": {
"key": "trgt",
"digest": "ylzep5nroxhzjff43gkc6fs25ydor7dd",
"digest": "uaowbumdens55465girwarokc46hwgco",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -178,7 +178,7 @@
},
"coverage_dropouts": {
"key": "coverage_dropouts",
"digest": "3el45hg36hlyx5cswr3dkvqfg644cvbn",
"digest": "3wfgwjflppb5tifrwycmjzy727p7wzyi",
"tests": [
{
"inputs": {
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4 changes: 2 additions & 2 deletions workflows/sample_analysis/sample_analysis.wdl
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Expand Up @@ -502,7 +502,7 @@ task trgt {
}

runtime {
docker: "~{runtime_attributes.container_registry}/trgt@sha256:8c9f236eb3422e79d7843ffd59e1cbd9b76774525f20d88cd68ca64eb63054eb"
docker: "~{runtime_attributes.container_registry}/trgt@sha256:07e9d2be1590fc1dd45e6e2a6b9f5869ee6d83f5a1ca47c8ea84e114b70573b6"
cpu: threads
memory: "4 GB"
disk: disk_size + " GB"
Expand Down Expand Up @@ -545,7 +545,7 @@ task coverage_dropouts {
}

runtime {
docker: "~{runtime_attributes.container_registry}/trgt@sha256:8c9f236eb3422e79d7843ffd59e1cbd9b76774525f20d88cd68ca64eb63054eb"
docker: "~{runtime_attributes.container_registry}/trgt@sha256:07e9d2be1590fc1dd45e6e2a6b9f5869ee6d83f5a1ca47c8ea84e114b70573b6"
cpu: threads
memory: "4 GB"
disk: disk_size + " GB"
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