From 49d412a51912482d020ac3d4e11f88dea277f5f7 Mon Sep 17 00:00:00 2001 From: roskamsh Date: Fri, 8 Nov 2024 09:16:48 +0000 Subject: [PATCH] change targene version to v0.11.1 in docs --- docs/src/examples/allofus.md | 2 +- docs/src/examples/gwas.md | 2 +- docs/src/examples/interactions.md | 2 +- docs/src/examples/phewas.md | 2 +- docs/src/overview.md | 2 +- docs/src/simulations/null_simulation.md | 2 +- docs/src/simulations/realistic_simulation.md | 2 +- docs/src/targene/overview.md | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/src/examples/allofus.md b/docs/src/examples/allofus.md index 08988002..c57c86bc 100644 --- a/docs/src/examples/allofus.md +++ b/docs/src/examples/allofus.md @@ -54,7 +54,7 @@ Here we have not specified any value for `ESTIMATORS_CONFIG`, and so the default Then TarGene can then be run on the AoU Researcher Workbench as follows: ```bash -nextflow run https://github.com/TARGENE/targene-pipeline -r v0.12.0 -profile gls,allofus +nextflow run https://github.com/TARGENE/targene-pipeline -r v0.11.1 -profile gls,allofus ``` By default, this will generate results in the `results/` directory in your `Cloud Analysis Terminal`. Once complete, you can upload these to your Workspace bucket using the following command: diff --git a/docs/src/examples/gwas.md b/docs/src/examples/gwas.md index be34d8fb..2172f87c 100644 --- a/docs/src/examples/gwas.md +++ b/docs/src/examples/gwas.md @@ -52,5 +52,5 @@ Finally, the `ESTIMATORS_CONFIG = "wtmle--glm"` defines the estimation strategy. The GWAS can then be run as follows: ```bash -nextflow run https://github.com/TARGENE/targene-pipeline -r v0.12.0 -profile local +nextflow run https://github.com/TARGENE/targene-pipeline -r v0.11.1 -profile local ``` \ No newline at end of file diff --git a/docs/src/examples/interactions.md b/docs/src/examples/interactions.md index 0bc95ad4..506ecd89 100644 --- a/docs/src/examples/interactions.md +++ b/docs/src/examples/interactions.md @@ -55,5 +55,5 @@ params { As usual, the pipeline can then be run as follows: ```bash -nextflow run https://github.com/TARGENE/targene-pipeline -r v0.12.0 -profile local +nextflow run https://github.com/TARGENE/targene-pipeline -r v0.11.1 -profile local ``` diff --git a/docs/src/examples/phewas.md b/docs/src/examples/phewas.md index 58dc368e..be54f005 100644 --- a/docs/src/examples/phewas.md +++ b/docs/src/examples/phewas.md @@ -46,5 +46,5 @@ params { And the command-line to be run: ```bash -nextflow run https://github.com/TARGENE/targene-pipeline -r v0.12.0 -profile local +nextflow run https://github.com/TARGENE/targene-pipeline -r v0.11.1 -profile local ``` diff --git a/docs/src/overview.md b/docs/src/overview.md index 10da556a..dab218bc 100644 --- a/docs/src/overview.md +++ b/docs/src/overview.md @@ -10,7 +10,7 @@ nextflow run https://github.com/TARGENE/targene-pipeline/ -r TARGENE_VERSION -en where: -- `TARGENE_VERSION` is the latest TarGene version, e.g. `v0.12.0` +- `TARGENE_VERSION` is the latest TarGene version, e.g. `v0.11.1` - `WORKFLOW_NAME` is any of the [TarGene workflows](@ref "Project Configuration") - `P` is an optional [Nextflow profile](https://www.nextflow.io/docs/latest/config.html) describing the computing platform (see [Platform Configuration](@ref)). diff --git a/docs/src/simulations/null_simulation.md b/docs/src/simulations/null_simulation.md index 54a681f8..81a4ccaa 100644 --- a/docs/src/simulations/null_simulation.md +++ b/docs/src/simulations/null_simulation.md @@ -11,7 +11,7 @@ The goal of the Null Generating Process is to result in the theoretical null hyp To run the null simulation, the `NULL_SIMULATION` entry should be added to the Nextflow command-line as follows ```bash -nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.12.0 -entry NULL_SIMULATION +nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.11.1 -entry NULL_SIMULATION ``` ## Output diff --git a/docs/src/simulations/realistic_simulation.md b/docs/src/simulations/realistic_simulation.md index 75e913b3..64471f19 100644 --- a/docs/src/simulations/realistic_simulation.md +++ b/docs/src/simulations/realistic_simulation.md @@ -23,7 +23,7 @@ The second requirement for the simulation to be realistic is that the density es To run the null simulation, the `REALISTIC_SIMULATION` entry should be added to the Nextflow command-line as follows ```bash -nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.12.0 -entry REALISTIC_SIMULATION +nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.11.1 -entry REALISTIC_SIMULATION ``` ## Output diff --git a/docs/src/targene/overview.md b/docs/src/targene/overview.md index f32ead57..e1ba0278 100644 --- a/docs/src/targene/overview.md +++ b/docs/src/targene/overview.md @@ -17,7 +17,7 @@ An overview of the workflow is presented in the following diagram. ## Example Run Command ```bash -nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.12.0 -profile local -resume +nextflow run https://github.com/TARGENE/targene-pipeline/ -r v0.11.1 -profile local -resume ``` We now describe step by step how to setup a TarGene run configuration.