From 4e4e83b8b80446e3d69c1b26d1171d09e57ee770 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Thu, 27 Jul 2023 14:50:18 -0400 Subject: [PATCH 1/3] update default docker for busco to GAR docker image. also exposed optional Int inputs cpu and memory --- tasks/quality_control/task_busco.wdl | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/tasks/quality_control/task_busco.wdl b/tasks/quality_control/task_busco.wdl index dd1bd9106..23b60edde 100644 --- 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 From 4741c48878c74f16571b59564d57c95faad46dc3 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Thu, 27 Jul 2023 15:14:09 -0400 Subject: [PATCH 2/3] update CI --- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 1e87a2e47..0b3445d2e 100644 --- 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 index 81de00e75..21c5feba9 100644 --- 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 From eba090d941914befa2688704ba5b23f9599f7b8b Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Fri, 28 Jul 2023 12:08:31 -0400 Subject: [PATCH 3/3] added a harmless return to the README.md simply so I can get the PR to update --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 10103286c..499546885 100644 --- 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).**