--target can point to file directly

[michael-kotliar]

If --target points to the file, --index and --data are ignored.
Output filenames are fixed to RELI.stats and RELI.overlaps

[ernstki]

Misha, what's the purpose of this (the Version: 0.0.2)? I like the idea of having examples for "Build," "Pull," and "Run," but I'm trying to understand why the version tag cannot simply be latest.

[michael-kotliar]

If our CWL file uses latest then after updating docker container, the inputs in CWL file should be updated too. To better control the correspondence between CWL and Docker I'd rather use more specific versions instead of latest

[michael-kotliar]

Btw, try to rebuild Dockerfile. I guess, it should me much smaller, then the original one.

[ernstki]

@michael-kotliar If Xiaoting was okay with the changes to the -target parameter, then I'll probably need to ask you to re-apply those to a new branch and resubmit a PR on GitHub.

Please leave CMakeLists.txt in your working directory without committing it next time. I'd like to stick with standard (GNU) build tools, and we don't use CLion, so our tools don't have built-in support for CMake.

On our internal GitLab server I'm currently working through a few issues merging Xiaoting's changes that write the RSIDs of overlapping SNPs to an output file. I'll close this PR to signal that we're ready for you to fork again and re-submit a PR. Apologies for the inconvenience; we're still learning. :)

[michael-kotliar]

Sure, no problem. Meanwhile, I'll add some other commits to this branch :)