From eb52a37fe2b9d6658eb22cfc044b9114ccfe3297 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 9 Aug 2023 20:05:10 +1000 Subject: [PATCH 1/2] Reorder upload excludes --- application/pipeline-stacks/oncoanalyser/assets/run.sh | 2 +- application/pipeline-stacks/star-align-nf/assets/run.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/application/pipeline-stacks/oncoanalyser/assets/run.sh b/application/pipeline-stacks/oncoanalyser/assets/run.sh index e32604a..c175493 100755 --- a/application/pipeline-stacks/oncoanalyser/assets/run.sh +++ b/application/pipeline-stacks/oncoanalyser/assets/run.sh @@ -405,8 +405,8 @@ upload_data() { aws s3 sync \ --no-progress \ --no-follow-symlinks \ - --exclude='software/*' \ --exclude='assets/*' \ + --exclude='software/*' \ --exclude='work/*' \ ./ "${output_dir}/" } diff --git a/application/pipeline-stacks/star-align-nf/assets/run.sh b/application/pipeline-stacks/star-align-nf/assets/run.sh index ace164d..44f77ac 100755 --- a/application/pipeline-stacks/star-align-nf/assets/run.sh +++ b/application/pipeline-stacks/star-align-nf/assets/run.sh @@ -246,8 +246,8 @@ upload_data() { aws s3 sync \ --no-progress \ --no-follow-symlinks \ - --exclude='software/*' \ --exclude='assets/*' \ + --exclude='software/*' \ --exclude='work/*' \ ./ "${output_dir}/" } From afe552e1846062539605f72024e504f0b70771b4 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 9 Aug 2023 20:05:40 +1000 Subject: [PATCH 2/2] Exclude .nextflow/ from pipeline upload --- application/pipeline-stacks/oncoanalyser/assets/run.sh | 1 + application/pipeline-stacks/star-align-nf/assets/run.sh | 1 + 2 files changed, 2 insertions(+) diff --git a/application/pipeline-stacks/oncoanalyser/assets/run.sh b/application/pipeline-stacks/oncoanalyser/assets/run.sh index c175493..a92a43d 100755 --- a/application/pipeline-stacks/oncoanalyser/assets/run.sh +++ b/application/pipeline-stacks/oncoanalyser/assets/run.sh @@ -405,6 +405,7 @@ upload_data() { aws s3 sync \ --no-progress \ --no-follow-symlinks \ + --exclude='.nextflow/*' \ --exclude='assets/*' \ --exclude='software/*' \ --exclude='work/*' \ diff --git a/application/pipeline-stacks/star-align-nf/assets/run.sh b/application/pipeline-stacks/star-align-nf/assets/run.sh index 44f77ac..8ce3bbc 100755 --- a/application/pipeline-stacks/star-align-nf/assets/run.sh +++ b/application/pipeline-stacks/star-align-nf/assets/run.sh @@ -246,6 +246,7 @@ upload_data() { aws s3 sync \ --no-progress \ --no-follow-symlinks \ + --exclude='.nextflow/*' \ --exclude='assets/*' \ --exclude='software/*' \ --exclude='work/*' \