AmpliconArchitect related paths must be absolute not relative

[SPPearce]

Description of the bug

The AmpliconArchitect related processes use this structure to set an environment variable: export AA_DATA_REPO=${params.aa_data_repo} without staging the files in that path into the work directory. If given an absolute path, this works, but if a relative path is given then the pipeline will fall over with a non-obvious failure message ending in :

ERROR:root:#TIME 1679058301.012 interval_list: Unable to open interval file "data_repo/GRCh38/". Traceback (most recent call last): File "~/.nextflow/assets/nf-core/circdna/bin/amplified_intervals.py", line 154, in <module> bamFileb2b = b2b.bam_to_breakpoint(bamFile, coverage_stats=cstats) File "~/.nextflow/assets/nf-core/circdna/bin/bam_to_breakpoint.py", line 129, in __init__ self.median_coverage(window_list=coverage_windows) File "~/.nextflow/assets/nf-core/circdna/bin/bam_to_breakpoint.py", line 540, in median_coverage coverage_stats_file = open(hg.DATA_REPO + "/coverage.stats", "a") IOError: [Errno 2] No such file or directory: 'data_repo/coverage.stats'

I see several ways to fix this:

• Ensure that an absolute path is provided, and fail otherwise.
• Convert the relative path to an absolute path.
• Pass the folder into the folder to stage it (this would be my preferred solution, and possibly is required for other cases than just giving a relative path rather than an absolute one).

Command used and terminal output

No response

Relevant files

No response

System information

No response

[DSchreyer]

Thanks for bringing this to my attention. I will note this down in the documentation and when running ampliconarchitect.

[DSchreyer]

Included in the newest release