User: a.james
a.james • 190
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Posts by a.james
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2
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... I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110 ...
written 22 days ago by
a.james • 190
0
votes
1
answer
114
views
1
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... I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110 ...
written 22 days ago by
a.james • 190
2
votes
1
answer
114
views
1
answer
... Dear All,
I have tried using java expression to capture all secondary files from STAR aligner in CWLtools version from 2018 October and 2019 February.
**On 2018 October version it is running successfully without any issues**, whereas on **2019 February version it is throwing error.**
Here is wha ...
written 22 days ago by
a.james • 190
0
votes
0
answers
85
views
0
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... Hello All,
I have a CWL workflow with 7 steps. And fourth step takes input from 2nd and 3rd step. How would I specify this dependency in CWL.
For example the workflow looks like following,
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
i ...
written 5 weeks ago by
a.james • 190
0
votes
0
answers
142
views
0
answers
... Dear All,
I am using CWL workflow in toil. And it is not recognising the path environment, which otherwise is fine. I mean, if I run the workflow as `cwltool` it is finishing successfully. When I try it in Toil it is not recognising the path `env`.
The command line tool: `sp.cwl`
cwlVersio ...
written 8 weeks ago by
a.james • 190
1
vote
1
answer
165
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1
answers
... Hello Tom,
Thanks for the comment and possible solution. The current expression (yours), is throwing a glob error as follows,
I made a little change and it is now working fine.
glob:
${
var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:"";
if (inputs.outS ...
written 3 months ago by
a.james • 190
2
votes
1
answer
165
views
1
answer
... Hello All,
I wanted to get 2 BAM files from STAR.cwl tool, one sorted and one unsorted, for that I wrote the following expression.
outputs:
star_bam:
type: File
outputBinding:
glob: |
${
var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:" ...
written 3 months ago by
a.james • 190
• updated
3 months ago by
Pierre Lindenbaum ♦ 120k
1
vote
1
answer
225
views
1
answers
... Thanks Tom, this is working. I tried it to on `scatter workflow` with array of file and string as input. It got finished successfully
...
written 3 months ago by
a.james • 190
0
votes
1
answer
225
views
1
answers
... Hey, Sorry, it is an error , It should be writer.sh.
Is the script stored in a location that is referenced in your $PATH? Yes, it is store the place where it is being invoked.
A dirty but quick fix would be to just pass your script as an argument in inputs. >> I did not quite understand what ...
written 3 months ago by
a.james • 190
3
votes
1
answer
225
views
1
answer
... Dear All,
I have small Shell script to write the lines in a file to another file
writer.sh
#!/usr/bin/env bash
infile=$1
outfile=$2
while read line
do
echo $line >> "$outfile"
done < "$infile"
I converted it for CWL as following, `writer.cwl`
...
written 3 months ago by
a.james • 190
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