User: a.james

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a.james170
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Germany
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21 hours ago
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4 years, 7 months ago
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a******@dkfz-heidelberg.de

Posts by a.james

<prev • 70 results • page 1 of 7 • next >
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Comment: C: CWL for star for multiple bam files with javascript expression
... 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.james170
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CWL for star for multiple bam files with javascript expression
... 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:" ...
cwl written 2 days ago by a.james170 • updated 1 day ago by Pierre Lindenbaum117k
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Comment: C: CWL to write into for writing lines one from one file to new file
... 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.james170
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Comment: C: CWL to write into for writing lines one from one file to new file
... 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.james170
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CWL to write into for writing lines one from one file to new file
... 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 < "$infile" I converted it for CWL as following, `writer.cwl` ...
cwl written 17 days ago by a.james170
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CWL toil-cwl-runner for two samples, could not find a error log and reason for failure
... Dear All, I am using CWL toil-cwl-runner for two samples on my CWL workflow. The workflow is running forever, without any clear error logs and error message in the log files. This is how the `main_parell.cwl` where all the sample logistics and the parallelising are defined. #!/usr/bin/env cw ...
cwl written 21 days ago by a.james170
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Comment: C: CWL with R returns empty output directory with "Final process status is success"
... For those of you who would have similar issues. So, I have got the results now by making some minor changes. I changed the glob part from `$(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.james170
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Comment: C: CWL with R returns empty output directory with "Final process status is success"
... 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.james170
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Comment: C: CWL with R returns empty output directory with "Final process status is success"
... @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.james170
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Comment: C: CWL with R returns empty output directory with "Final process status is success"
... @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.james170

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