update default docker for busco to GAR docker image (#132)

* update default docker for busco to GAR docker image. also exposed optional Int inputs cpu and memory * update CI * added a harmless return to the README.md simply so I can get the PR to update
theiagen · Jul 28, 2023 · 7cc91fb · 7cc91fb
1 parent ee71277
commit 7cc91fb
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -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).**

diff --git a/tasks/quality_control/task_busco.wdl b/tasks/quality_control/task_busco.wdl
@@ -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
   }
@@ -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

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -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

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -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