Create conda environments under the analysis directory by default for 'make_fastqs' & 'run_qc' - #1180
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pjbriggs merged 3 commits intoJul 20, 2026
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If the location for conda environments is not explicitly supplied or set in the configuration then default is now to create within the analysis directory.
If the location for conda environments is not explicitly supplied or set in the configuration then default is now to create within the analysis directory.
pjbriggs
added
enhancement
QC pipeline
Fastq generation
dependencies
Conda envs in the 'run_qc' command were defaulting to the working directory for the pipeline execution (rather than the analysis directory as originally intended).
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Updates the
make_fastqsandrun_qccommands so that by default create any conda environments are now created in a subdirectory of the current analysis directory (specifically<ANALYSIS_DIR>/__conda/envs).This default will still be overridden by locations supplied either via the command line, or via the configuration settings. The change is intended to prevent old or unwanted environments being left lying around after analyses have completed.