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plasmidfinder task bugfix and updates #191

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merged 2 commits into from
Sep 19, 2023
Merged

plasmidfinder task bugfix and updates #191

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40744ea
plasmidfinder task updates: decrease cpus to 2, memory to 8, and disk…
kapsakcj Sep 15, 2023
7851504
update CI
kapsakcj Sep 15, 2023
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14 changes: 7 additions & 7 deletions tasks/gene_typing/task_plasmidfinder.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ task plasmidfinder {
input {
File assembly
String samplename
Int cpu = 8
Int memory = 16
Int cpu = 2
Int memory = 8
String docker = "us-docker.pkg.dev/general-theiagen/staphb/plasmidfinder:2.1.6"
Int disk_size = 100
Int disk_size = 50
String? database
String? database_path
String? method_path
Expand Down Expand Up @@ -41,15 +41,15 @@ task plasmidfinder {
if [ ! -f results_tab.tsv ]; then
PF="No plasmids detected in database"
else
PF="$(tail -n +2 results_tab.tsv | cut -f 2 | sort | uniq -u | paste -s -d, - )"
PF="$(tail -n +2 results_tab.tsv | uniq | cut -f 2 | sort | paste -s -d, - )"
if [ "$PF" == "" ]; then
PF="No plasmids detected in database"
fi
fi
echo $PF | tee PLASMIDS
echo "$PF" | tee PLASMIDS

mv results_tab.tsv ~{samplename}_results.tsv
mv Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa
mv -v results_tab.tsv ~{samplename}_results.tsv
mv -v Hit_in_genome_seq.fsa ~{samplename}_seqs.fsa

>>>
output {
Expand Down
4 changes: 2 additions & 2 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Expand Up @@ -264,7 +264,7 @@
- path: miniwdl_run/call-merlin_magic/workflow.log
contains: ["wdl", "theiaprok_illumina_pe", "merlin", "done"]
- path: miniwdl_run/call-plasmidfinder/command
md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35
md5sum: 3b70033058bf91c04337e38bfd038b5a
- path: miniwdl_run/call-plasmidfinder/inputs.json
- path: miniwdl_run/call-plasmidfinder/outputs.json
- path: miniwdl_run/call-plasmidfinder/stderr.txt
Expand Down Expand Up @@ -556,7 +556,7 @@
- path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl
md5sum: 0bed8fb60786095843a67b1ad03051dc
- path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl
md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8
md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72
- path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl
md5sum: 8e8423b99d5cd3e92bb89b3c3211d432
- path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl
Expand Down
4 changes: 2 additions & 2 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 @@ -261,7 +261,7 @@
- path: miniwdl_run/call-merlin_magic/workflow.log
contains: ["wdl", "theiaprok_illumina_se", "merlin", "done"]
- path: miniwdl_run/call-plasmidfinder/command
md5sum: 61f7be9cfd36e3a48585e7f64cbcfe35
md5sum: 3b70033058bf91c04337e38bfd038b5a
- path: miniwdl_run/call-plasmidfinder/inputs.json
- path: miniwdl_run/call-plasmidfinder/outputs.json
- path: miniwdl_run/call-plasmidfinder/stderr.txt
Expand Down Expand Up @@ -526,7 +526,7 @@
- path: miniwdl_run/wdl/tasks/gene_typing/task_bakta.wdl
md5sum: 0bed8fb60786095843a67b1ad03051dc
- path: miniwdl_run/wdl/tasks/gene_typing/task_plasmidfinder.wdl
md5sum: 6ca295b4dcdbe95dd86516ba0a4073f8
md5sum: 8730e07b1c7ab9d2434a7838ddb1fc72
- path: miniwdl_run/wdl/tasks/gene_typing/task_prokka.wdl
md5sum: 8e8423b99d5cd3e92bb89b3c3211d432
- path: miniwdl_run/wdl/tasks/gene_typing/task_resfinder.wdl
Expand Down