Hello there!
I am a total newbie in CWL and I'm struggling to write a simple workflow counting words in input file and writing the number (and the number only!) in output file. To remove the file name from wc output I wrote this:
file.cwl:
cwlVersion: v1.0
class: CommandLineTool
requirements:
class: ShellCommandRequirement
inputs:
input_file:
type: File
outputs:
output_file:
type: File
outputBinding:
glob: output/output
stdout: output/output
baseCommand: wc
arguments:
- valueFrom: '-w'
shellQuote: false
position: 1
- valueFrom: input_file
shellQuote: false
position: 2
- valueFrom: '|'
shellQuote: false
position: 3
- valueFrom: 'awk'
shellQuote: false
position: 4
- valueFrom: '"'
shellQuote: false
position: 5
- valueFrom: '{print $1;}'
shellQuote: false
position: 6
- valueFrom: '"'
shellQuote: false
position: 7
file.yml:
input_file:
class: File
path: input/input
And I got error mapSubject '%s' value '%s' is not a dict and does not have a mapPredicate
What does it mean? What am I doing wrong?
Hello gultagr,
requirements:
class: ShellCommandRequirement
should be
requirements:
- class: ShellCommandRequirement
or
requirements:
ShellCommandRequirement: {}
You can also write the baseCommand and arguments this way:
baseCommand: []
arguments:
- wc
- -w
- $(inputs.input_file)
- '|'
- awk
- '{print $1;}'
Here is a simpler version, taking advantage of how wc changes its behavior when the input is piped in via stdin
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
inputs:
text: File
outputs:
number_of_words: stdout
stdin: $(inputs.text.path)
stdout: words # optional line, but gives the output a nicer file name
baseCommand: [ wc, -w ]
Thanks for the example. Just what I needed right now. Was trying to use stdin: $(inputs.text) instead of $(inputs.text.path). Also, interesting way to do a pipe using the arguments field instead of connecting wc and awk with a workflow.
Log in to answer this question.
Where is the bioinformatics part of your question?
Hello b.nota,
BioStars is the official Q&A site for the Common Workflow Language project -- this is done with permission and approval of Istvan Albert.
http://www.commonwl.org/#Support
Hello gultagr,
Can you edit your question and reformat your code? There should be a button in the interface that looks like "101 010"
I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: