From 4c6da77bc826a1d9475ac274033fbd4aa1c7f560 Mon Sep 17 00:00:00 2001 From: Mootor Date: Tue, 19 Jul 2022 19:42:06 -0700 Subject: [PATCH 1/3] Closes #50 - save_intermediate_files set to false by default --- CHANGELOG.md | 1 + config/default.config | 2 +- config/template.config | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 781ce7d..25e20ca 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ### Added - Add F16.config to enable F16 node compatibility ### Changed +- Set `save_intermediate_files` to false in default.config - Rename call-sSV.nf to main.nf - Standardize the repo structure based on NF pipeline template - Update README.md with resource locations and runtime of Delly v1.0.3 on different datasets and node types diff --git a/config/default.config b/config/default.config index 0e370f5..c18528f 100644 --- a/config/default.config +++ b/config/default.config @@ -14,7 +14,7 @@ params { max_memory = SysHelper.getAvailMemory() cache_intermediate_pipeline_steps = false - save_intermediate_files = true + save_intermediate_files = false ucla_cds = true diff --git a/config/template.config b/config/template.config index 3bcfc9d..b1e24bc 100755 --- a/config/template.config +++ b/config/template.config @@ -19,7 +19,7 @@ params { output_dir = "where/to/save/outputs/" - save_intermediate_files = true + save_intermediate_files = false verbose = false From 928f696ca12dfa4c3ec6fcd205d173b86cd3fc3f Mon Sep 17 00:00:00 2001 From: Mootor Date: Wed, 20 Jul 2022 15:06:17 -0700 Subject: [PATCH 2/3] remove save_intermediate_files argument from default.config --- config/default.config | 1 - 1 file changed, 1 deletion(-) diff --git a/config/default.config b/config/default.config index c18528f..efc249a 100644 --- a/config/default.config +++ b/config/default.config @@ -14,7 +14,6 @@ params { max_memory = SysHelper.getAvailMemory() cache_intermediate_pipeline_steps = false - save_intermediate_files = false ucla_cds = true From 28d9f83e3ee0293481ab0d807bf2388d0ef08bd7 Mon Sep 17 00:00:00 2001 From: Mootor Date: Wed, 20 Jul 2022 15:16:25 -0700 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 25e20ca..7d7c51b 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ### Added - Add F16.config to enable F16 node compatibility ### Changed -- Set `save_intermediate_files` to false in default.config +- Remove `save_intermediate_files` argument in default.config as it is already specified in template.config - Rename call-sSV.nf to main.nf - Standardize the repo structure based on NF pipeline template - Update README.md with resource locations and runtime of Delly v1.0.3 on different datasets and node types