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I have a program that wants me to input a fairly large list of files. So far I've been doing this but literally listing them out in array format (Ex: Array[File] files = ["a.fna", "b.fna", "c.fna", "d…
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Hello
I have encountered the following problem:
I have a workflow that contains (among others) the two tasks GetBwaVersion and MergeBamAlignment.
MergeBamAlignment takes as an input the outpu…
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The README file of sctools did not provide any installation proceduce to install the tool. The python pypi sctools only have old 0.1.6 version of sctools. Would you show how to install the lastest ver…
zhq90 updated
2 years ago
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I know I can specify the [instance types](https://aws.github.io/amazon-genomics-cli/docs/concepts/contexts/#instance-types) for a specific context, which are available to all tasks, but I would also l…
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at https://github.com/broadinstitute/cromwell/blame/develop/docs/Configuring.md#L184
add a note that the local backend should not run dockerized tasks, per
https://gatkforums.broadinstitute.org/wdl/…
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@ngaddis you did some sort of magic to create those snp id reference files and we should automate that.
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**miniwdl is tested on *Intel* macOS**, with a few specific setup steps:
- [ ] Install [Docker Desktop for Mac](https://docs.docker.com/docker-for-mac/install/)
- Use Docker's menu bar icon to sel…
mlin updated
5 months ago
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Hi,
Running a workflow on WSL/Ubuntu 20.04 using conda-installed Cromwell:
`cromwell run ngs-ubuntu-20-04/iletisim/warp/pipelines/broad/dna_seq/germline/single_sample/exome/local_newGCP_ExomeGer…
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I have a workflow that was previously registered on Dockstore via the "Register Custom Remote Workflows" route.
However, we recently re-organized our repository, and two changes that are relevant are…
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The `ScriptParser` class defines how a Nextflow script is executed. It essentially takes a Nextflow script and produces a Groovy class (i.e. `BaseScript`) which, when executed, builds the workflow DAG…