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[TheiaProk] Update amrfinderplus to v3.12.8; DB: v2024-05-02.2; reduce compute resources #514

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merged 4 commits into from
Jun 24, 2024
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[TheiaProk] Update amrfinderplus to v3.12.8; DB: v2024-05-02.2; reduce compute resources #514

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c2b6ae1
amrfinderplus updates: reduce cpus to 2 and memory to 8 and disk_size…
kapsakcj Jun 21, 2024
02bf597
Merge remote-tracking branch 'origin/main' into cjk-amrfinderplus-update
kapsakcj Jun 21, 2024
e6b9907
update CI
kapsakcj Jun 21, 2024
e11228c
update CI
kapsakcj Jun 21, 2024
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12 changes: 6 additions & 6 deletions tasks/gene_typing/drug_resistance/task_amrfinderplus.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@ task amrfinderplus_nuc {
Float? minid
Float? mincov
Boolean detailed_drug_class = false
Int cpu = 4
String docker = "us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:3.11.20-2023-09-26.1"
Int disk_size = 100
Int memory = 16
Int cpu = 2
String docker = "us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2"
Int disk_size = 50
Int memory = 8
Boolean hide_point_mutations = false
Boolean separate_betalactam_genes = false
}
Expand Down Expand Up @@ -55,7 +55,7 @@ task amrfinderplus_nuc {
if [[ -v amrfinder_organism ]] ; then
# always use --plus flag, others may be left out if param is optional and not supplied
amrfinder --plus \
--organism ${amrfinder_organism} \
--organism "${amrfinder_organism}" \
~{'--name ' + samplename} \
~{'--nucleotide ' + assembly} \
~{'-o ' + samplename + '_amrfinder_all.tsv'} \
Expand Down Expand Up @@ -198,7 +198,7 @@ task amrfinderplus_nuc {
docker: docker
disks: "local-disk " + disk_size + " SSD"
disk: disk_size + " GB"
preemptible: 0
preemptible: 1
maxRetries: 3
}
}
8 changes: 4 additions & 4 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
- wf_theiaprok_illumina_pe_miniwdl
files:
- path: miniwdl_run/call-amrfinderplus_task/command
md5sum: 51f02263973b62c5fc2fde0b45056231
md5sum: 6c2c570754a616e7ac032109d8ffe71c
- path: miniwdl_run/call-amrfinderplus_task/inputs.json
contains: ["assembly", "fasta", "organism", "test"]
- path: miniwdl_run/call-amrfinderplus_task/outputs.json
Expand All @@ -29,9 +29,9 @@
- path: miniwdl_run/call-amrfinderplus_task/task.log
contains: ["wdl", "theiaprok_illumina_pe", "amrfinderplus", "done"]
- path: miniwdl_run/call-amrfinderplus_task/work/AMRFINDER_DB_VERSION
md5sum: 54ebef28014734172bfeeb798d0e7873
md5sum: af6e77e015582e10a0cadb800726bb4b
- path: miniwdl_run/call-amrfinderplus_task/work/AMRFINDER_VERSION
md5sum: 8e8e52e7e47bb3f44f866b41fe825422
md5sum: 326a7d8c0e1f7435f5ae5c9153171036
- path: miniwdl_run/call-amrfinderplus_task/work/AMR_CLASSES
md5sum: b6017eebef847ac2471107ca6197b5c5
- path: miniwdl_run/call-amrfinderplus_task/work/AMR_CORE_GENES
Expand Down Expand Up @@ -551,7 +551,7 @@
- path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_abricate.wdl
md5sum: 0a8e80d9c835a712936eac2cc6e3a05d
- path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_amrfinderplus.wdl
md5sum: 3afe9dcac768bf6f62e8b69714ce8b86
md5sum: 654c31055b807b3cd2aee9d5ceeea766
- path: miniwdl_run/wdl/tasks/gene_typing/annotation/task_bakta.wdl
md5sum: 0bed8fb60786095843a67b1ad03051dc
- path: miniwdl_run/wdl/tasks/gene_typing/plasmid_detection/task_plasmidfinder.wdl
Expand Down
8 changes: 4 additions & 4 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
- wf_theiaprok_illumina_se_miniwdl
files:
- path: miniwdl_run/call-amrfinderplus_task/command
md5sum: 51f02263973b62c5fc2fde0b45056231
md5sum: 6c2c570754a616e7ac032109d8ffe71c
- path: miniwdl_run/call-amrfinderplus_task/inputs.json
contains: ["assembly", "fasta", "organism", "test"]
- path: miniwdl_run/call-amrfinderplus_task/outputs.json
Expand All @@ -29,9 +29,9 @@
- path: miniwdl_run/call-amrfinderplus_task/task.log
contains: ["wdl", "theiaprok_illumina_se", "amrfinderplus", "done"]
- path: miniwdl_run/call-amrfinderplus_task/work/AMRFINDER_DB_VERSION
md5sum: 54ebef28014734172bfeeb798d0e7873
md5sum: af6e77e015582e10a0cadb800726bb4b
- path: miniwdl_run/call-amrfinderplus_task/work/AMRFINDER_VERSION
md5sum: 8e8e52e7e47bb3f44f866b41fe825422
md5sum: 326a7d8c0e1f7435f5ae5c9153171036
- path: miniwdl_run/call-amrfinderplus_task/work/AMR_CLASSES
md5sum: b6017eebef847ac2471107ca6197b5c5
- path: miniwdl_run/call-amrfinderplus_task/work/AMR_CORE_GENES
Expand Down Expand Up @@ -516,7 +516,7 @@
- path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_abricate.wdl
md5sum: 0a8e80d9c835a712936eac2cc6e3a05d
- path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_amrfinderplus.wdl
md5sum: 3afe9dcac768bf6f62e8b69714ce8b86
md5sum: 654c31055b807b3cd2aee9d5ceeea766
- path: miniwdl_run/wdl/tasks/gene_typing/annotation/task_bakta.wdl
md5sum: 0bed8fb60786095843a67b1ad03051dc
- path: miniwdl_run/wdl/tasks/gene_typing/plasmid_detection/task_plasmidfinder.wdl
Expand Down