User: a.james

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a.james190
Reputation:
190
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Location:
Germany
Last seen:
1 day, 18 hours ago
Joined:
4 years, 10 months ago
Email:
a******@dkfz-heidelberg.de

Posts by a.james

<prev • 75 results • page 1 of 8 • next >
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Answer: A: CWLtools version problem with usage of secondary files and java expression
... I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110 ...
written 22 days ago by a.james190
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Comment: C: CWLtools version problem with usage of secondary files and java expression
... I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110 ...
written 22 days ago by a.james190
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CWLtools version problem with usage of secondary files and java expression
... 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 ...
cwl written 22 days ago by a.james190
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How to step dependency in a step based on the output from 2 previous steps in CWL workflow
... 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 ...
cw written 5 weeks ago by a.james190
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CWL in toil
... 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 ...
toil cwl written 8 weeks ago by a.james190
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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 3 months ago by a.james190
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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 3 months ago by a.james190 • updated 3 months ago by Pierre Lindenbaum120k
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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 3 months ago by a.james190
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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 3 months ago by a.james190
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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 3 months ago by a.james190

Latest awards to a.james

Scholar 22 days ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 25 days ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 9 weeks ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 3 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 14 months ago, created a question with more than 1,000 views. For GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 14 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 14 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 17 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 23 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 23 months ago, created a question with more than 1,000 views. For How to find the frame shift information from fusion gene sequence
Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq output from RNA-seq
Popular Question 2.4 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Student 2.7 years ago, asked a question with at least 3 up-votes. For ALL RNA-seq publicly available data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Scholar 2.8 years ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Supporter 2.9 years ago, voted at least 25 times.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Pathway Graphs for gene set from RNA-seq
Popular Question 3.4 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 3.4 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data

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