From 4eebefce2651381291a37d744e22d9d82f323677 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Mon, 13 May 2024 00:17:36 -0700 Subject: [PATCH 1/2] update default docker in aws_test to use ghcr --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index baf8562..64f7e07 100644 --- a/nextflow.config +++ b/nextflow.config @@ -18,7 +18,7 @@ profiles { } params { // docker image parameters, see nextflow_schema.json for details - main_pipeline_docker = "sagebionetworks/genie:develop" + main_pipeline_docker = "ghcr.io/sage-bionetworks/genie:develop" main_release_utils_docker = "sagebionetworks/main-genie-release-utils" find_maf_artifacts_docker = "sagebionetworks/genie-artifact-finder" create_data_guide_docker = "sagebionetworks/genie-data-guide" From 81195c5f77127722b8b0101a7adf631168b5bb52 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Mon, 13 May 2024 00:30:13 -0700 Subject: [PATCH 2/2] correct run commands --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b7f88b6..8010087 100644 --- a/README.md +++ b/README.md @@ -72,30 +72,30 @@ Note that all the docker parameters have set default docker containers based on * **Only validate** files on test pipeline ``` - nextflow -profile aws_test run main.nf --process_type only_validate -with-docker sagebionetworks/genie:latest + nextflow run main.nf -profile aws_test --process_type only_validate -with-docker sagebionetworks/genie:latest ``` * Processes **non-mutation** files on test pipeline ``` - nextflow -profile aws_test run main.nf --process_type main_process -with-docker sagebionetworks/genie:latest + nextflow run main.nf -profile aws_test --process_type main_process -with-docker sagebionetworks/genie:latest ``` * Processes **mutation** files on test pipeline ``` - nextflow -profile aws_test run main.nf --process_type maf_process --create_new_maf_db -with-docker sagebionetworks/genie:latest + nextflow run main.nf -profile aws_test --process_type maf_process --create_new_maf_db -with-docker sagebionetworks/genie:latest ``` * Runs **processing** and **consortium** release (including data guide creation) on test pipeline ``` - nextflow -profile aws_test run main.nf --process_type consortium_release --create_new_maf_db -with-docker sagebionetworks/genie:latest + nextflow run main.nf -profile aws_test --process_type consortium_release --create_new_maf_db -with-docker sagebionetworks/genie:latest ``` * Runs **public** release (including data guide creation) on test pipeline ``` - nextflow -profile aws_test run main.nf --process_type public_release -with-docker sagebionetworks/genie:latest + nextflow run main.nf -profile aws_test --process_type public_release -with-docker sagebionetworks/genie:latest ``` ### Testing