add pod5 version 0.3.23

[sage-wright]

this is a simple docker w/ the pod5 tool which enables command-line examination of pod5 files

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

It looks like the tests worked

#10 [test 2/4] RUN pod5 --help &&     pod5 --version
#10 0.247 usage: pod5 [-h] [-v]
#10 0.247             {convert,inspect,merge,repack,subset,filter,recover,update,view}
#10 0.247             ...
#10 0.247 
#10 0.247 **********      POD5 Tools      **********
#10 0.247 
#10 0.247 Tools for inspecting, converting, subsetting and formatting POD5 files
#10 0.247 
#10 0.247 optional arguments:
#10 0.247   -h, --help            show this help message and exit
#10 0.247   -v, --version         Show pod5 version and exit.
#10 0.247 
#10 0.247 Example: pod5 convert fast5 input.fast5 --output output.pod5
#10 0.442 Pod5 version: 0.3.23
#10 DONE 0.5s

#11 [test 3/4] RUN wget https://github.com/nanoporetech/dorado/raw/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
#11 0.056 --2025-03-19 18:59:57--  https://github.com/nanoporetech/dorado/raw/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
#11 0.064 Resolving github.com (github.com)... 140.82.112.4
#11 0.067 Connecting to github.com (github.com)|140.82.112.4|:443... connected.
#11 0.163 HTTP request sent, awaiting response... 302 Found
#11 0.257 Location: https://raw.githubusercontent.com/nanoporetech/dorado/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 [following]
#11 0.257 --2025-03-19 18:59:57--  https://raw.githubusercontent.com/nanoporetech/dorado/release-v0.7/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
#11 0.257 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
#11 0.259 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
#11 0.268 HTTP request sent, awaiting response... 200 OK
#11 0.271 Length: 15888 (16K) [application/octet-stream]
#11 0.271 Saving to: ‘dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5’
#11 0.271 
#11 0.271      0K .......... .....                                      100% 46.8M=0s
#11 0.272 
#11 0.272 2025-03-19 18:59:57 (46.8 MB/s) - ‘dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5’ saved [15888/15888]
#11 0.272 
#11 DONE 0.3s

#12 [test 4/4] RUN pod5 view . --include "read_id, channel" --output summary.tsv &&     pod5 subset . --summary summary.tsv --columns channel
#12 1.033 /usr/local/lib/python3.9/site-packages/pod5/tools/pod5_subset.py:234: MapWithoutReturnDtypeWarning: Calling `map_elements` without specifying `return_dtype` can lead to unpredictable results. Specify `return_dtype` to silence this warning.
#12 1.033   targets.select(pl.col(PL_DEST_FNAME).unique())
#12 1.039 Parsed 1 targets
#12 1.[366](https://github.com/StaPH-B/docker-builds/actions/runs/13954580858/job/39062391255?pr=1255#step:8:372) Calculated 1 transfers
#12 1.667 
Subsetting:   0%|          | 0/1 [00:00<?, ?Files/s]
#12 1.671 
channel-1.pod5:   0%|          | 0/1 [00:00<?, ?Reads/s]
#12 1.677 
                                                        
Subsetting: 100%|##########| 1/1 [00:00<00:00, 93.75Files/s]
#12 1.779 Done
#12 DONE 1.8s

[erinyoung]

The contents of summary.tsv are as follows.

If this is the expected result, we can merge this and get this deployed.

$ cat summary.tsv 
read_id channel
c4b111a0-90eb-436e-b6b1-cf14dee1fb93    1

[sage-wright]

That's the anticipated output!

[erinyoung]

Perfect!

[erinyoung]

Thank you for putting this together!

You can check the status of the deployment here : https://github.com/StaPH-B/docker-builds/actions/runs/13975395470