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🐳 update sentieon dockers #149

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merged 2 commits into from
Feb 24, 2025
+18 −18
Merged

🐳 update sentieon dockers #149

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0d60e14
:whale: update sentieon dockers
dmiller15 Feb 17, 2025
7b64e75
update docker table
dmiller15 Feb 17, 2025
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16 changes: 8 additions & 8 deletions docs/dockers_sentieon_alignment.md
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Original file line number Diff line number Diff line change
@@ -12,14 +12,14 @@ picard_collectgvcfcallingmetrics.cwl|pgc-images.sbgenomics.com/d3b-bixu/picard:2
samtools_head.cwl|staphb/samtools:1.15
samtools_idxstats_xy_ratio.cwl|pgc-images.sbgenomics.com/d3b-bixu/samtools:1.9
samtools_split.cwl|pgc-images.sbgenomics.com/d3b-bixu/samtools:1.9
sentieon_HsMetricAlgo.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_ReadWriter.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_WgsMetricsAlgo.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_bqsr.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_bwa_sort.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_dedup.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_haplotyper.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_run_agg_metrics.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_HsMetricAlgo.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_ReadWriter.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_WgsMetricsAlgo.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_bqsr.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_bwa_sort.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_dedup.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_haplotyper.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_run_agg_metrics.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
t1k.cwl|pgc-images.sbgenomics.com/d3b-bixu/t1k:v1.0.5
tabix_index.cwl|pgc-images.sbgenomics.com/d3b-bixu/samtools:1.9
untar_indexed_reference_2.cwl|None
4 changes: 2 additions & 2 deletions docs/dockers_sentieon_gvcf.md
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Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@ TOOL|DOCKER
gatk_indexfeaturefile.cwl|pgc-images.sbgenomics.com/d3b-bixu/gatk:4.1.7.0R
picard_collectgvcfcallingmetrics.cwl|pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R
samtools_idxstats_xy_ratio.cwl|pgc-images.sbgenomics.com/d3b-bixu/samtools:1.9
sentieon_ReadWriter.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_haplotyper.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
sentieon_ReadWriter.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
sentieon_haplotyper.cwl|pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
untar_indexed_reference_2.cwl|None
verifybamid_contamination_conditional.cwl|pgc-images.sbgenomics.com/d3b-bixu/verifybamid:1.0.2
2 changes: 1 addition & 1 deletion tools/sentieon_HsMetricAlgo.cwl
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Original file line number Diff line number Diff line change
@@ -53,7 +53,7 @@ requirements:
}
}
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_ReadWriter.cwl
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Original file line number Diff line number Diff line change
@@ -15,7 +15,7 @@ requirements:
coresMin: $(inputs.cpu_per_job)
ramMin: $(inputs.mem_per_job * 1000)
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_WgsMetricsAlgo.cwl
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Original file line number Diff line number Diff line change
@@ -50,7 +50,7 @@ requirements:
}
}
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_bqsr.cwl
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Original file line number Diff line number Diff line change
@@ -19,7 +19,7 @@ requirements:
coresMin: $(inputs.cpu_per_job)
ramMin: $(inputs.mem_per_job)
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_bwa_sort.cwl
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Original file line number Diff line number Diff line change
@@ -21,7 +21,7 @@ requirements:
ramMin: |
$(inputs.mem_per_job * 1000)
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_dedup.cwl
View file
Original file line number Diff line number Diff line change
@@ -20,7 +20,7 @@ requirements:
coresMin: $(inputs.cpu_per_job)
ramMin: $(inputs.mem_per_job * 1000)
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE
2 changes: 1 addition & 1 deletion tools/sentieon_haplotyper.cwl
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Original file line number Diff line number Diff line change
@@ -21,7 +21,7 @@ requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: ResourceRequirement
coresMin: $(inputs.cpu)
ramMin: $(inputs.ram * 1000)
2 changes: 1 addition & 1 deletion tools/sentieon_run_agg_metrics.cwl
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Original file line number Diff line number Diff line change
@@ -59,7 +59,7 @@ requirements:
}
}
- class: DockerRequirement
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112.01_hifi
dockerPull: pgc-images.sbgenomics.com/hdchen/sentieon:202112_hifi_patched
- class: EnvVarRequirement
envDef:
- envName: SENTIEON_LICENSE