John Didion
John Didion
I am trying to build the docker image on a MacBook Pro with M1 Max Pro chip. I try using both `arm64` and `native` for the `--architecture` option. In either...
I am guessing that openmp is not available for arch64? ``` #0 82.63 /usr/bin/ld: ../contrib/WFA2-lib/lib/libwfacpp.a(wavefront_compute_affine.o): in function `wavefront_compute_affine': #0 82.63 wavefront_compute_affine.c:(.text+0xa08): undefined reference to `GOMP_parallel' #0 82.63 /usr/bin/ld: ../contrib/WFA2-lib/lib/libwfacpp.a(wavefront_compute_affine.o): in...
I have a workflow that uses `fastp` for both read trimming and report generation. If read trimming is skipped, then the alignment step does not depend on `fastp` completion before...
The attached workflow returns the correct output sometimes and other times does not. In the failure case it is because the input file is not correctly staged in the task's...
When I pack a conformance test that contains an enum type (e.g. https://github.com/common-workflow-language/cwl-v1.2/blob/main/tests/anon_enum_inside_array.cwl) the packed workflow turns the enum symbols into URI fragments. The symbols should not be modified. ```...
For workflows with tools that are specified in-line and don't have their own IDs (e.g. see https://github.com/common-workflow-language/cwl-v1.2/blob/main/tests/timelimit2-wf.cwl), the parser gives the tools randomly generated IDs. Importantly, those IDs are not...
The typical behavior of `cwltool --pack` is to set the ID of the main tool/workflow to `#main` and then prefix all it's input and output IDs with `#main/`. However, when...
I have a feedstock build that is failing (https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=368340) due to the fact that a `GITHUB_TOKEN` environment variable is required by one of the sbt plugins. Is there a way...
Refining of reads is not discussed in the paper or the README (that I can find). It would be helpful to know what it means and when it's necessary.
It would be nice to have summary information shown at the end of the output, such as: Total reads: XXX Correctable reads: XXX (x%) Reads corrected: XXX (x%) Total bases...