[BUG] output without suffix, and no loom published

[atomnh]

Describe the bug
When I run the PBMC example of scenic_multirun (v0.26.0) as the Docs indicated, The publication process has some issues, files under out/data/ without suffix, like this:

sample_data.10x_PBMC.single_sample.final_output. -> scenic_multirun/test/64/17c197846f07aa2ecd44492afd6e73/sample_data.SC__SCANPY__MARKER_GENES.h5ad
sample_data.SINGLE_SAMPLE. -> scenic_multirun/test/a5/68de6af1c4ee49eebbf96ba219237c/sample_data.SINGLE_SAMPLE.loom

And the file loom file cannot export successful with warning:
Jul-03 16:53:32.742 [Task monitor] WARN nextflow.processor.PublishDir - Failed to publish file:
single_sample_test/work/8e/b8586d6505dc4cb69d680d0d0644e6/1k_pbmc_v3_chemistry.SC__H5AD_TO_LOOM.loom; to: single_sample_test/out/loom/1k_pbmc_v3_chemistry.SCope_output.loom [link] -- See log file for details

To Reproduce
Steps to reproduce the behavior:

1. Configure with these options:

I follow the tutorials in the Docs (https://vsn-pipelines-examples.readthedocs.io/en/latest/PBMC10k_multiruns.html) to adjust the configure file

2. Run using this entry point:

nextflow -C pbmc10k.vsn-pipelines.complete.config run vib-singlecell-nf/vsn-pipelines -entry single_sample

3. See error:

filenames of files under out/data are lack of suffixes, and no loom file was exported to out/loom

Expected behavior
I want the filename under out/data to be completed as it supposed to be:
sample_data.10x_PBMC.single_sample.final_output.h5ad -> scenic_multirun/test/64/17c197846f07aa2ecd44492afd6e73/sample_data.SC__SCANPY__MARKER_GENES.h5ad
sample_data.SINGLE_SAMPLE.loom -> scenic_multirun/test/a5/68de6af1c4ee49eebbf96ba219237c/sample_data.SINGLE_SAMPLE.loom

Please complete the following information:

• OS: CentOS v7
• Nextflow Version: 20.10.0.5
• vsn-pipelines Version: 0.26

[cflerin]

Thanks for the report @atomnh. This should be fixed in the latest release.