Fix pixi Singularity template PATH environment

[munishchouhan]

Summary

• The conda/pixi:v1 Singularity template incorrectly referenced $MAMBA_ROOT_PREFIX (a micromamba-specific variable) in the %environment section. Since pixi never sets this variable, installed executables (e.g. fastqc, multiqc) were not found in $PATH.
• Fixed by sourcing the pixi-generated /shell-hook.sh in %environment, which correctly activates the pixi environment (PATH, CONDA_PREFIX, etc.)
• Removed the unnecessary exec "$@" append to /shell-hook.sh — this is a Docker entrypoint pattern that has no effect in Singularity containers.

Context

fixes #1035

Changes

• singularityfile-conda-file.txt — Replaced export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" with . /shell-hook.sh and removed the unnecessary exec "$@" line
• PixiHelperTest.groovy — Added assertions verifying shell-hook sourcing and no MAMBA_ROOT_PREFIX reference

Test plan

• PixiHelperTest passes
• Verified manually: fastqc found at /opt/wave/.pixi/envs/default/bin/fastqc inside a pixi-built Singularity container

[munishchouhan]

tested locally:

% docker run --rm --privileged --platform linux/amd64 kaczmarj/apptainer exec oras://hrma017/fastqc:fastqc-0.12.1--f3e77eeaf62fa693 which fastqc                  
INFO:    Downloading oras image
/opt/wave/.pixi/envs/default/bin/fastqc