adhoc¶

Execute an ad hoc analysis

The adhoc template assists in running one-liners - possibly on a set of input files

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: no help defined

mode: operation mode: seq, sequential: process the input files one by one; par, parallel: process the input files in parallel (use with -j); all: process all input files at once (use $^ in adhoc_process) and simple: Ignore input files, just execute adhoc_process once.

type: set

default: simple

optional: True
name_sed: A sed expression which can be used to derive the output file name for each input file (excluding the path). The sed expression is executed for each input file name, and the result is available as $t in the $(adhoc_process) statement. Make sure that you use single quotes when specifying this on the command line

type: string

default: s/a/a/

optional: True
output_dir: Output subdirectory

type: directory

default: .

optional: True
process: Command to execute for each input file. The path to the input file is available as $< and the output file as $t. (it is not mandatory to use both parameters, for example “cat $< > output” would concatenate all files into one big file

type: string

default: echo “needs a sensbile command”

optional: True
touch: use touch files to track if input files have changed.

type: set

default: T

optional: True