Nextflow
https://www.nextflow.io/docs/latest/getstarted.html
process - basic processing unit (maybe a stage)
channels/queues - data input and output streams of sort
watchPath - for a watch on file events
script: (script block) can be a string or groovy code that returns a string
‘ ’ / ” ” / ’’’ ‘’’ / ””” “””
bash-like variable expansion in single vs double quote (variables defined in nexflow file scope)
for system variables use single quotes
exec: (exec block) groovy code to be executed
ErrorStrategies
‘retry’ - more exploration needed
‘maxRetries’ - number of retries for an instance of a process (or can be called a task)
‘maxErrors’ - number of errors for all instances of a process (all tasks)
stages - processes
supported languages - shebang in the script
Nextflow variables
!varName is nextflow variable in shell ($varName is bash variable in shell)
$varName is valid everywhere
Workflow
Workflow is where it starts
processes are run in workflow and can be pipelined as per the need
input and output channels can be used to chain processes together
scripts are where the execution happens, can be bash, python or any other scripting language
https://carpentries-incubator.github.io/workflows-nextflow/08-configuration/index.html