User: a.james
a.james • 170
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- 4 years, 7 months ago
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Posts by a.james
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0
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... 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 1 day ago by
a.james • 170
1
vote
1
answer
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... 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 2 days ago by
a.james • 170
• updated
1 day ago by
Pierre Lindenbaum ♦ 117k
1
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... 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 17 days ago by
a.james • 170
0
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... 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 17 days ago by
a.james • 170
3
votes
1
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... 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 < "$infile"
I converted it for CWL as following, `writer.cwl`
...
written 17 days ago by
a.james • 170
0
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72
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... Dear All,
I am using CWL toil-cwl-runner for two samples on my CWL workflow. The workflow is running forever, without any clear error logs and error message in the log files.
This is how the `main_parell.cwl` where all the sample logistics and the parallelising are defined.
#!/usr/bin/env cw ...
written 21 days ago by
a.james • 170
1
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answers
... For those of you who would have similar issues.
So, I have got the results now by making some minor changes. I changed the glob part from `$(inputs.outputdir)` to `runtime.outdir`. And so now the CWL tool is now collecting the output files, where it is been executed.
...
written 23 days ago by
a.james • 170
1
vote
1
answer
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... Yes, so I need to update the post. Now I have outputs in CWL, by changing the initial directory requirement into,
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing: [ $(inputs.outputdir) ]
And , by changing the type of `outputdir` into `director ...
written 24 days ago by
a.james • 170
0
votes
1
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207
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... @Tom, the command line tool for my RScript look like : `Rscript HIF_scorefinder.R /cluster/home/user/Projects/Kjo_proct/pocKj /cluster/home/user/Projects/Kjo_proct/HypScore1`. This successfully gives out all I need as output. The output files or the results stores up in this `/cluster/home/user/Pr ...
written 25 days ago by
a.james • 170
0
votes
1
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207
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... @Michael
Thanks for the reply, The R script independly runs a commandlinetool tool without any errors. But even with new addons from your solution. It is finished successfully without `arguments`. But the output directory is empty.
But when I run with arguments it is throwing errors.
Error i ...
written 28 days ago by
a.james • 170
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