User: Tom

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Tom250
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Bielefeld University, CeBiTec, Germany
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Posts by Tom

<prev • 56 results • page 1 of 6 • next >
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Comment: C: Perform one basecommand fot multiple files and get output for each file in CWL
... Hi Maria, The workflow is missing a space character between "-" and "class" in the `requirements` section. Also, since the `unzip` step uses `scatter`, it will return an array as output. For this reason the `compiled_class` entry in the `outputs` section of the workflow needs to be of `type: File[ ...
written 21 hours ago by Tom250
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Comment: C: CWL docker command user
... You have to remove the `dockerPull: broadinstitute/gatk:4.1.2.0` line from your code. The broadinstitutes docker container is causing the issue, so you don't want to use that one anymore. I used the Dockerfile i posted below. I usually put my containers on [docker hub,][1] but the easiest solution ...
written 2 days ago by Tom250
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Comment: C: CWL docker command user
... Hi Daiana! Did the answer below help you? Please feel free to ask if you have further questions. Coming from a biology background, it takes me a lot of time (and questions in this forum) to figure some of the bioinformatics stuff out. So i'm very sympathetic to anyone needing more elaborate explan ...
written 3 days ago by Tom250
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Answer: A: Perform one basecommand fot multiple files and get output for each file in CWL
... Hello fellow pipeline enthusiast! To my knowledge, it is not possible to do what you ask using only a command line tool and stdout. Two alternate solutions come to mind: 1. Change your command line tool so it will only unzip and return a single file ([or use this one][1]). Embed said command line ...
written 3 days ago by Tom250
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Comment: C: bedtools sort -faidx in CWL
... I have not yet used bedtools, so i'm not sure i understand correctly. Can you spell out the names of the files which bedtools needs to access for the line you have given in the beginning? I guess one is `g38.fasta.fai`. But what are the names of the other files? ...
written 7 days ago by Tom250
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Comment: C: CWL :Append the ref input used in toolkit
... It is really difficult to understand what the issue is. Maybe try giving us a specific example of what you are working on. What software do you want to run? Can you post the current version of your command line tool, even if it doesn't work? What is the file you have trouble passing to the tool? If ...
written 7 days ago by Tom250
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Comment: C: CWL docker command user
... The dockerfile: FROM ibmjava ARG GATK_VERSION=4.1.2.0 RUN apt-get update -y && apt-get install -y \ unzip \ wget \ python WORKDIR /software RUN wget https://github.com/broadinstitute/gatk/releases/do ...
written 7 days ago by Tom250
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Answer: A: CWL docker command user
... I am pretty sure this is just an issue of spark/docker (see [stackoverflow][1]) and not related to CWL. I experience the same issue when trying to use the broadinstitute gatk container to run your command line tool. The thread on stackoverflow provides several solutions. I made a docker container f ...
written 7 days ago by Tom250
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Comment: C: CWL docker command user
... I'm not sure this problem is caused by lacking permissions. But then again i have no experience using GATK. Would you mind sharing the docker container and the command line tool? ...
written 12 days ago by Tom250
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Answer: A: CWL join two dimensional file array output
... I believe there is no built-in functionality for what you are asking. I would suggest adding an `ExpressionTool` between the two workflow steps. I just tested the following and it seems to work: [in the steps section of your workflow] arrayBusiness: run: class: Exp ...
written 4 weeks ago by Tom250

Latest awards to Tom

Scholar 4 weeks ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 3 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 4 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 4 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Supporter 4 months ago, voted at least 25 times.
Scholar 4 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 4 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Student 12 months ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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