1.2.0: Merge pull request #51 from DKFZ-ODCF/lsf-env-none-fix

• Minor: Updated to miniconda3:4.10.3 base container, because the previous version (4.9.2) didn't build anymore.
• Minor: Use -env none for "lsf" cluster profile. Local environment should not be copied. This probably caused problems with the old "dkfzModules" environment profile.
• Patch: Require Nextflow >= 22.07.1, which fixes an LSF memory request bug. Added options for per-job memory requests to "lsf" profile in nextflow.config.
• Patch: Remove unnecessary *_BINARY variables in scripts. Binaries are fixed by Conda/containers.
• Patch: Needed to explicitly set conda.enabled = True with newer Nextflow

+publishMode (rellink) & -dkfzModules

• Minor: Added --publishMode option to allow user to select the Nextflow publish mode. Default: rellink. Note that the former default was symlink, but as this change is considered negligible we classified the change as "minor".
• Minor: Removed dkfzModules profile. Didn't work well and was originally only for development. Please use 'conda', 'singularity' or 'docker'. The container-based environments provide the best reproducibility.
• Patch: Switched from Travis to CircleCI for continuous integration.

1.0.1

• Fix retry memory.
• More descriptive job name.
• Better final message.

First fully functional version

First fully functional version of a Nextflow workflo for BAM-to-FASTQ conversion and optional subsequent FASTQ sorting.

• This is the replacement for the old RoddyBamToFastq workflow and includes stability fixes and generally a better usability.
• The code is validated with integration and unit tests at Github (continous integration via Travis)
• The job-environments are release as Docker containers to Github releases (continuous delivery).