Matthias De Smet

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3. Cromwell question: localization of reference files

Hi Jason, That's exactly the case, the fasta/fai/dict are in another directory than the bwa indexes. Putting all the inputs in the same directory does fix the issue. I'd like to avoid putting many ...

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• April 16, 2021 15:40
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Cromwell question: localization of reference files

Hi, First of all, sorry for asking a question thats already been asked 100's of times, but I can't seem to find an answer that applies. I'm trying to run an alignment task in docker using bwa-mem2,...

• Matthias De Smet
• April 16, 2021 08:03
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3. Using fofn files in docker

FYI, fixed by letting the task that creates the fofn run on the host instead of in docker   Matthias

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• April 16, 2021 07:23
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3. Using fofn files in docker

Hi Jason,   Thanks for the reply! Might I refer to a github issue for more info? https://github.com/openwdl/wdl/issues/452 I'll also shoot you an e-mail with the workflow, perhaps it might be more ...

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• Edited April 02, 2021 14:54
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Using fofn files in docker

Hi, I've got a task that runs in docker and creates a fofn file. This fofn is then to be used as input for another task (not in docker). However, the filepaths in the fofn are relative to the cromw...

• Matthias De Smet
• April 02, 2021 11:39
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3. map Array[File] to Object[samplename, Array[Files] based on filename

To get back to this, awesome idea, worked like a charm!

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• October 28, 2020 15:05
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3. map Array[File] to Object[samplename, Array[Files] based on filename

That’s actually a great idea. I’ll have to try it. I will get back to you tomorrow. Thanks for the tip! Matthias

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• October 27, 2020 20:49
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3. map Array[File] to Object[samplename, Array[Files] based on filename

Hi Tiffany,   Thanks for the examples, but those don't really fix my question. I'm starting from an array of files which contain all uBam's for all lanes of a flowcell for alle samples. I'm trying ...

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• October 24, 2020 11:23
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