Update image dependencies

[crosenth]

Steps

1. Run regression tests and save output:

% nextflow -quiet run main.nf -params-file test/minimal/params.json -profile docker --container gha_image
% nextflow -quiet run main.nf -params-file test/its/params.json -profile docker --container gha_image
% nextflow -quiet run main.nf -params-file test/noindex/params.json -profile docker --container gha_image
% nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -profile docker --container gha_image
% nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -profile docker --container gha_image
% nextflow -quiet run main.nf -params-file test/minimal/params.json -profile docker --container gha_image --manifest test/minimal/manifest.csv
% nextflow -quiet run main.nf -params-file test/its/params.json -profile docker --container gha_image --manifest test/its/manifest.csv
% nextflow -quiet run main.nf -params-file test/noindex/params.json -profile docker --container gha_image --manifest test/noindex/manifest.csv
% nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -profile docker --container gha_image --manifest test/single/manifest.csv
% nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -profile docker --container gha_image --manifest test/single/manifest.csv

2. Update base image and benjjneb/dada2 version
   a. Base image: rocker/r-ubuntu:24.04
   b. benjjneb/dada2 version to v1.26 release here: https://github.com/nhoffman/dada2-nf/blob/master/docker/Dockerfile#L3
3. Commit and run git tag dev and git push origin master --tags
4. Confirm CI/CD runs to completion and new image is created: ghcr.io/nhoffman/dada2-nf:dev
5. Update nextflow.config to point to dev image: https://github.com/nhoffman/dada2-nf/blob/master/nextflow.config#L10
6. Run regression tests again and compare/confirm outputs
7. Update requirements.txt dependencies and pin all deps
8. Update Infernal and vsearch deps in docker/install_infernal_and_easel.sh and docker/install_vsearch.sh
9. Commit and run git tag dev and git push origin master --tags
10. Confirm CI/CD runs to completion and new image is created: ghcr.io/nhoffman/dada2-nf:dev
11. Run regression tests again and compare/confirm outputs
12. Remove dev tag: git tag -d dev && git push -d origin dev

Optional:

1. Confirm all dependencies are needed and being used
2. Remove apt-get install vsearch (it should be installed already with docker/install_vsearch.sh)

[dhoogest]

Took the first step and hit a snag related to infernal/easel install: https://github.com/nhoffman/dada2-nf/actions/runs/20038570499/job/57466511447. Will followup on that later on!

[dhoogest]

Okay now into the constraints in Ubuntu 24.04 related to system level pip use. This error is encountered:

#18 [14/15] RUN pip3 install -U pip wheel
#18 0.327 error: externally-managed-environment
#18 0.327 
#18 0.327 × This environment is externally managed
#18 0.327 ╰─> To install Python packages system-wide, try apt install
#18 0.327     python3-xyz, where xyz is the package you are trying to
#18 0.327     install.
#18 0.327     
#18 0.327     If you wish to install a non-Debian-packaged Python package,
#18 0.327     create a virtual environment using python3 -m venv path/to/venv.
#18 0.327     Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
#18 0.327     sure you have python3-full installed.
#18 0.327     
#18 0.327     If you wish to install a non-Debian packaged Python application,
#18 0.327     it may be easiest to use pipx install xyz, which will manage a
#18 0.327     virtual environment for you. Make sure you have pipx installed.
#18 0.327     
#18 0.327     See /usr/share/doc/python3.12/README.venv for more information.
#18 0.327 
#18 0.327 note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
#18 0.327 hint: See PEP 668 for the detailed specification.
#18 ERROR: process "/bin/sh -c pip3 install -U pip wheel" did not complete successfully: exit code: 1

@nhoffman @crosenth think we should move ahead with virtualenv install or just --break-system-packages? Note that we could also go for uv managed installs.

[dhoogest]

Okay now into the constraints in Ubuntu 24.04 related to system level pip use. This error is encountered:

#18 [14/15] RUN pip3 install -U pip wheel
#18 0.327 error: externally-managed-environment
#18 0.327 
#18 0.327 × This environment is externally managed
#18 0.327 ╰─> To install Python packages system-wide, try apt install
#18 0.327     python3-xyz, where xyz is the package you are trying to
#18 0.327     install.
#18 0.327     
#18 0.327     If you wish to install a non-Debian-packaged Python package,
#18 0.327     create a virtual environment using python3 -m venv path/to/venv.
#18 0.327     Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
#18 0.327     sure you have python3-full installed.
#18 0.327     
#18 0.327     If you wish to install a non-Debian packaged Python application,
#18 0.327     it may be easiest to use pipx install xyz, which will manage a
#18 0.327     virtual environment for you. Make sure you have pipx installed.
#18 0.327     
#18 0.327     See /usr/share/doc/python3.12/README.venv for more information.
#18 0.327 
#18 0.327 note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
#18 0.327 hint: See PEP 668 for the detailed specification.
#18 ERROR: process "/bin/sh -c pip3 install -U pip wheel" did not complete successfully: exit code: 1

@nhoffman @crosenth think we should move ahead with virtualenv install or just --break-system-packages? Note that we could also go for uv managed installs.

I'm trying out the uv option with 7b47362 - build succeeded for me locally, but tbd on the smoke tests.

[dhoogest]

Okay clean build, however the pipeline hit a fastq parsing issue seen here: https://github.com/nhoffman/dada2-nf/actions/runs/20046562240/job/57493236960

@crosenth I think I saw this in a brief test on garuda - maybe to do with newer nextflow version?

[dhoogest]

Note that tests other than the test/its/params.json appear to work fine in local testing. This is the only one with cutadapt in play, and I was able to confirm that that test passes with nextflow 25.04.0 (the version in play at the point of the last successful build)

[dhoogest]

Pretty sure this is the reason for the broken test (incorporated in nf 25.10.0).

nextflow-io/nextflow#6268

Most likely just a problem with the reads we are using (I don't recall if we truncated these or what) - will need to look into that and potentially rework the sample and fastq lists involved

[dhoogest]

Okay all good following a change to the ITS test params to require non-zero seq lengths following trim (which is what we already had in the prod params). Think we're good to go with #92