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update default docker for busco to GAR docker image #132

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Jul 28, 2023
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1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# Public Health Bioinformatics (PHB)

Bioinformatics workflows for characterization, epidemiology and sharing of pathogen genomes.

**More information about the steps undertaken in these workflows is available via the [Theiagen Public Resources Documentation](https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566).**
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8 changes: 5 additions & 3 deletions tasks/quality_control/task_busco.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,9 @@ task busco {
input {
File assembly
String samplename
String docker = "ezlabgva/busco:v5.3.2_cv1" # not available on us-docker.pkg.dev/general-theiagen
String docker = "us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1"
Int memory = 8
Int cpu = 2
Int disk_size = 100
Boolean eukaryote = false
}
Expand Down Expand Up @@ -50,8 +52,8 @@ task busco {
}
runtime {
docker: "~{docker}"
memory: "8 GB"
cpu: 2
memory: "~{memory} GB"
cpu: cpu
disks: "local-disk " + disk_size + " SSD"
disk: disk_size + " GB"
preemptible: 0
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Expand Up @@ -566,7 +566,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/task_bbduk.wdl
md5sum: 90e49f4e4568393cf8d1f8720a4772ad
- path: miniwdl_run/wdl/tasks/quality_control/task_busco.wdl
md5sum: eba8518737396c0655e390a49c0a5a55
md5sum: 0f8b3fbca316cb940a61b2c3cdf6ebab
- path: miniwdl_run/wdl/tasks/quality_control/task_cg_pipeline.wdl
md5sum: c8e7ae1ed0fff7b14731228db80c6b30
- path: miniwdl_run/wdl/tasks/quality_control/task_fastp.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -536,7 +536,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/task_bbduk.wdl
md5sum: 90e49f4e4568393cf8d1f8720a4772ad
- path: miniwdl_run/wdl/tasks/quality_control/task_busco.wdl
md5sum: eba8518737396c0655e390a49c0a5a55
md5sum: 0f8b3fbca316cb940a61b2c3cdf6ebab
- path: miniwdl_run/wdl/tasks/quality_control/task_cg_pipeline.wdl
md5sum: c8e7ae1ed0fff7b14731228db80c6b30
- path: miniwdl_run/wdl/tasks/quality_control/task_fastp.wdl
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