Merge pull request #164 from Plant-Food-Research-Open/docs/rev

Added explicit revision param to docs
Plant-Food-Research-Open · Oct 25, 2024 · abd4695 · abd4695
2 parents fe7b8fc + 62e19f5
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diff --git 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`
 

diff --git 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 <version> \
    -profile <docker/singularity/.../institute> \
    --input assemblysheet.csv \
    --outdir <OUTDIR>

diff --git 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,<docker/singularity> --outdir <OUTDIR>
+        nextflow run plant-food-research-open/assemblyqc -revision <version> -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git 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,<docker/singularity> --outdir <OUTDIR>
+        nextflow run plant-food-research-open/assemblyqc -revision <version> -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git 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 <version> --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: