Updated docs to include -r flag

README.md

@@ -57,6 +57,7 @@ At minimum, a file with proteins as evidence is also required. Now, you can run
 
 ```bash
 nextflow run plant-food-research-open/genepal \
+  -revision <version> \
   -profile <docker/singularity/.../institute> \
   --input assemblysheet.csv \
   --protein_evidence proteins.faa \

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

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

docs/output.md

@@ -199,10 +199,7 @@ The completeness of the annotations is checked with [BUSCO](https://gitlab.com/e
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `genepal_software_mqc_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Parameters used by the pipeline run: `params.json`.
-- `multiqc/`
-  - `multiqc_report.html`: A MultiQC report which includes QC statistics, software versions and references.
-  - `multiqc_data/`: MultiQC data files
-  - `multiqc_plots/`: MultiQC plots
+- `multiqc_report.html`: A MultiQC report which includes QC statistics, software versions and references.
 
 </details>
 

docs/usage.md

@@ -163,6 +163,7 @@ The typical command for running the pipeline is as follows:
 
 ```bash
 nextflow run plant-food-research-open/genepal \
+  -revision <version> \
   -profile <docker/singularity/.../institute> \
   --input assemblysheet.csv \
   --protein_evidence proteins.faa \
@@ -190,7 +191,7 @@ 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/genepal -profile docker -params-file params.yaml
+nextflow run plant-food-research-open/genepal -revision main -profile docker -params-file params.yaml
 ```
 
 with:

nextflow.config

@@ -274,7 +274,7 @@ validation {
     defaultIgnoreParams = ["genomes"]
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run $manifest.name -revision <version> -profile <docker/singularity/.../institute> --input assemblysheet.csv --protein_evidence proteins.faa --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"