From 27a8d3b4d3081a987615f0b75464c385466e3147 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 25 Oct 2024 15:09:31 +1300 Subject: [PATCH 1/2] Added explicit revision param to docs --- README.md | 1 + conf/test.config | 2 +- conf/test_full.config | 2 +- docs/usage.md | 4 ++-- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4737e2e8..8d9b478e 100644 --- a/README.md +++ b/README.md @@ -102,6 +102,7 @@ Now, you can run the pipeline using: ```bash nextflow run plant-food-research-open/assemblyqc \ + -revision \ -profile \ --input assemblysheet.csv \ --outdir diff --git a/conf/test.config b/conf/test.config index 2417719d..e86178f3 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run plant-food-research-open/assemblyqc -profile test, --outdir + nextflow run plant-food-research-open/assemblyqc -revision -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 2eadbf9b..818e1c86 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run plant-food-research-open/assemblyqc -profile test_full, --outdir + nextflow run plant-food-research-open/assemblyqc -revision -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/usage.md b/docs/usage.md index 20f10823..3e8b314b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -136,7 +136,7 @@ All the modules have been tested to work on a single machine with 10 CPUs + 32 G The typical command for running the pipeline is as follows: ```bash -nextflow run plant-food-research-open/assemblyqc --input ./assemblysheet.csv --outdir ./results -profile docker +nextflow run plant-food-research-open/assemblyqc -revision --input ./assemblysheet.csv --outdir ./results -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -160,7 +160,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < The above pipeline run specified with a params file in yaml format: ```bash -nextflow run plant-food-research-open/assemblyqc -profile docker -params-file params.yaml +nextflow run plant-food-research-open/assemblyqc -revision main -profile docker -params-file params.yaml ``` with: From 62e19f584b769e9cd48763bd962a69005acd8248 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 25 Oct 2024 15:12:21 +1300 Subject: [PATCH 2/2] Updated changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42bd00e1..b53c1203 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.2.0dev - [15-Oct-2024] +## v2.2.0dev - [25-Oct-2024] ### `Added` @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 1. Fixed a bug where Gene score distribution graph did not appear correctly [#125](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/125) 2. Increased memory requirement for `DNADIFF` to avoid SLURM OOM kills with exit code 2 [#141](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/141) +3. Documented the use explicit use of `-revision` parameter [#160](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/160) ### `Dependencies`