Commit 08ac3503 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Add ansi-log false option. Add notes how to cope with github access exceptions

parent 973cd027
......@@ -3,25 +3,33 @@
In this exercise you will run your first nextflow workflow from github, modify
it and see the resume capabilities of nextflow.
### Setup
## Setup
Create a new directory for workflow execution and change into it
### Run workflow
## Run workflow
Execute the hello-world workflow from the ag-computational-bio/nf-hello github repository:
~~~~
nextflow run ag-computational-bio/nf-hello
nextflow run -ansi-log false ag-computational-bio/nf-hello
~~~~
> **_NOTE_** It may happen that github rejects access to the repository due to
high anonymous acess during the course. In that case you can replace
`ag-computational-bio/nf-hello` with `/var/tmp/nf-hello` for this and subsequent
steps to use a local copy on your training machine.
>**_NOTE_** For demonstration purposes the `-ansi-log false` option is passed to
nextflow. For future calls this is not required.
### Question
What files and directories are created in your current directory? What is their purpose?
Hint: Also check for hidden files.
### Modify workflow
## Modify workflow
Clone the workflow in your current working directory:
......@@ -41,7 +49,7 @@ nextflow run nf-hello -resume
What do you see in the output of nextflow? What does it mean?
### Cleanup
## Cleanup
Check your runs with the `nextflow log` command and cleanup all runs with the
`nextflow clean` command.
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