Michael L Heuer

[ch-10] Updates to ADAM code examples

5

I noted some ADAM code examples in the 2nd edition need updating: `adam-submit transform` → `adam-submit transformAlignments` `sc.broadcast(new TwoBitFile(...)` → `sc.loadReferenceFile` All the region join calls are different, joins are...

Support for graal native-image

13

Hello, I am tracking a runtime error with zstd-jni when attempting to build a [GraalVM native-image](https://www.graalvm.org/docs/reference-manual/native-image/) that includes `com.github.luben:zstd-jni:jar:1.4.4-7:runtime` as a dependency. https://github.com/heuermh/dishevelled-bio/issues/24 I am still rather new to native-image,...

Output file("*.foo") returns a single file or list

3

## Bug report Capturing wildcard files in an ```output:``` block ```nextflow process split_foo_gz { input: set sample, file(foo) from foos output: set sample, file("*.foo.gz") into splitFoos ... ``` appears to...

Missing dependency on google-cloud-storage from google-cloud-nio

2

It appears `google-cloud-nio` is missing a dependency on `google-cloud-storage`, at least when used in Maven `runtime` scope. #### Steps to reproduce pom.xml: ``` com.google.cloud libraries-bom 25.2.0 pom import ... com.google.cloud...

After removing patches from the bioconda recipe for 0.23.0, the ADAM startup scripts still don't resolve correctly when symlinks ``` + source /opt/conda/bin/activate /opt/conda/conda-bld/adam_1522259566898/_t_env + /bin/bash -x -e /opt/conda/conda-bld/adam_1522259566898/test_tmp/run_test.sh +...

Improve Ensembl VEP mapping to TranscriptEffect

1

See https://github.com/bigdatagenomics/bdg-formats/issues/202 https://github.com/heuermh/bdg-formats/blob/docs/docs/source/transcript-effects.md