Resolve full path to output directory in Nextflow command

[nwiltsie]

The combination of these two code chunks...

tool-NFTest/nftest/NFTestENV.py

Line 23 in d096b96

self.NFT_OUTPUT = os.getenv('NFT_OUTPUT', default='./')

tool-NFTest/nftest/NFTestCase.py

Lines 103 to 105 in d096b96

	output_directory_with_case = Path(self._env.NFT_OUTPUT)/self.name_for_output
	output_directory_arg = f"--{self.output_directory_param_name} " \
	f"{output_directory_with_case}"

... and python's behavior of stripping leading ./s from paths...

In [2]: Path("./") / "foo"
Out[2]: PosixPath('foo')

... results in passing bare relative paths for the --output_dir argument, which triggers uclahs-cds/pipeline-Nextflow-config#59 for me:

NXF_WORK=././test/work nextflow run ./main.nf -c /hot/code/nwiltsie/pipelines/pipeline-align-DNA/test/global.config -c ./test/a_mini_n2-picard.config --output_dir a_mini_n2-picard

We should resolve all of those relative paths before launching Nextflow.

[yashpatel6]

Agreed, also building on this, we should resolve all paths for the config files in the Nextflow run command