Parameters

Alternative parameter file formats

More parameters can be specified using the next format

example.csv

  parameter1, parameter2
  value11,    value21
  value12,    value22
  value13,    value23

Alternatively, parameters can be specified in the +.properties+ style. The parameters file also should have the +.properties+ extension.

example.properties

  parameter1 = value11, value12, value13
  parameter2 = value21, value22, value23

Values for the workflow to iterate over can be passed as CSV file with parameter names in the header (a-zA-Z0-9 and underscore, starting with a-zA-Z) and parameter values in each row. Use quotes to escape commas, e.g. "a,b".

Each value is one of the following:

• a string

• a Freemarker template documentation

• a series i..j (where i and j are two integers), meaning from i to j including i and j

• a list of ';' separated values (may contain templates)

Joining parameter files

You can combine multiple parameter files: the values will be 'natural joined' based on overlapping columns.

Example with two or more parameter files:

  molgenis --path path/to/workflow -p f1.csv -p f2.csv -w workflow.csv

f1.csv (white space will be trimmed):

  p0,  p2
  x,   1
  y,   2

f2.csv (white space will be trimmed):

  p1,  p2,    p3,     p4
  v1,  1..2,  a;b,    file${p2}

Merged and expanded result for f1.csv + f2.csv:

  p0,  p1,  p2,   p3,   p4
  x,   v1,  1,    a,    file1 
  x,   v1,  1,    b,    file1
  y,   v1,  2,    a,    file2
  y,   v1,  2,    b,    file2

More complex parameter examples can combine values with template, as following:

  foo=    item1 , item2
  bar=    ${foo}, item3
  number= 123

Here, variable 'bar' has two values of variable 'foo'.

Specifying workflow in parameters file

Alternatively to specifying workflow in the command-line using '-w' or '--workflow', workflow can be present as a parameter in parameters.csv file:

  workflow, parameter1, parameter2
  workflow.csv, value1, value2

Lists of parameters

Parameters can be specified in several parameter files. To understand how 'list' parameter specification works, let's consider the case with 2 parameter files and 1 protocol.

parameters1.csv

  project , sample
  project1, sample1
  project1, sample2
  project1, sample3

parameters2.csv

  chr
  chr1
  chr2
  chr3

The example protocol looks like

protocol1.sh

  #!/bin/sh
  #string project
  #list sample
  #list chr
  for s in "${sample[@]}"
  do
    echo $s
    for c in "${chr[@]}"
    do
         echo $c
    done
  done

Here, 'sample' and 'chr' parameters are coming from 2 different parameter files. Both parameters are specified as 'list' in the protocol. These lists of parameters will not be combined, since they are coming from different parameters files. The generated parameters lists will have the next look:

  #!/bin/sh
  #string project
  #list sample
  #list chr
  for s in "sample1" "sample2" "sample3"
  do
    echo $s
    for c in "chr1" "chr2" "chr3"
    do
         echo $c
    done
  done

If users want to combine lists that coming from separated files, lists should be declared on the same line, like

  list sample, chr

It will produce one list with all possible combination of parameters:

  sample1, chr1
  sample1, chr2
  sample1, chr3
  sample2, chr1
  sample2, chr2
  sample2, chr3
  sample3, chr1
  sample3, chr2
  sample3, chr3

It is not the desired behaviour in the considered protocol:

  #!/bin/sh
  #string project
  #list sample, chr
  for s in "sample1" "sample1" "sample1" "sample2" "sample2" "sample2" "sample3" "sample3" "sample3"
  do
    echo $s
    for c in "chr1" "chr2" "chr3" "chr1" "chr2" "chr3" "chr1" "chr2" "chr3"
    do
         echo $c
    done
  done