diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md index d7f215427f52eda0f8f99f23363f051f4dfb5271..89bd3876fe10a419b46e6ec0a6b94cbb89541bcf 100644 --- a/docs/source/getting_started/Working.md +++ b/docs/source/getting_started/Working.md @@ -11,10 +11,12 @@ The three commands that are the core of BiTIA's functionality are: #### 1. Running commands ```bash -$ bitia run "samtools convert foo.fa#http://example.com/foo.fa" +$ bitia run "samtools convert <foo.fa|http://example.com/foo.fa>" ``` The above code will: -- Add the given command `samtools run foo.fa#http://example.com/foo.fa` into a pipeline file. +- Checks for the input file `foo.fa` in the current working directory +- Download the input file from given link `http://example.com/foo.fa` and name it as `foo.fa` +- Add the given command `samtools convert <foo.fa|http://example.com/foo.fa` into a pipeline file. - Extract the current working directory with the pipeline as a zip file that contains a unique hash and send it to the server `public.bitia.link` - The BiTIA runner in the server will execute the pipeline by: - Installing the given command `samtools`