Merge branch 'master' into dev-v2.1-#287

TheJacksonLaboratory · Jan 19, 2022 · be2c2ab · be2c2ab
2 parents 04285ef + 33ba660
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diff --git a/docs/run_on_sumner.md b/docs/run_on_sumner.md
@@ -76,7 +76,7 @@ Each rMATS comparison must be specified with a comparison name as well as the `s
 
 This config file will be specific to your user and analysis. **You do not need to edit the pipeline code to configure the pipeline**. Descriptions of all possible parameters and their default values can be found [here](usage.md#all-available-parameters) and [here](https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/03c977a4a5b386a1ea31c8aae78592432e38f3a2/nextflow.config). 
 
-To create your own custom config (to specify your input parameters) you can copy and edit this [example config](https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/6ff6a5d3a629b2a9923f99c8266f7120409f4371/NF_splicing_pipeline.config) file. 
+To create your own custom config (to specify your input parameters) you can copy and edit this [example config](https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/d5ef6327fd3773484ecd1f0cdd593531e47cff39/NF_splicing_pipeline.config) file. 
 
 **VERY IMPORTANT NOTES***
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -216,11 +216,11 @@ Other:
                                 (default: false)
     --error_strategy            Mode of pipeline handling failed processes.
                                 Possible values: 'terminate', 'finish', 'ignore', 'retry'.
-                                Check nextflow documnetation for detailed descriptions of each mode:
+                                Check nextflow documentation for detailed descriptions of each mode:
                                 https://www.nextflow.io/docs/latest/process.html#process-page-error-strategy
                                 Set this parameter in the main.pbs, on the command line, or see NF_splicing_pipeline.config
                                 example (does not work like normal config param)
-                                This does not overwrited CloudOS config, which is set to:
+                                This does not overwrite CloudOS config, which is set to:
                                 'errorStrategy = { task.exitStatus in [3,9,10,14,143,137,104,134,139] ? 'retry': 'ignore'}
                                 (default (non-cloudos): 'finish')
     --cleanup                   This option will enable nextflow work folder cleanup upon pipeline successfull