Conversation
- Add Dockerfiles for skesa, blast, bwa, samtools, picard, trimmomatic, quast - Wrap all tool invocations in job_creator.py with _singularity_exec() - Wrap makeblastdb, bwa index, samtools faidx in referencer.py with _singularity_exec() - Add singularity and containers config sections to configExample.json - Update test_config.py to expect singularity/containers config keys - Slim environment.yml to python-only (tools now run via Singularity containers) Co-Authored-By: Claude <noreply@anthropic.com>
- build_containers_stage.yml: manual workflow_dispatch trigger, builds all 7 tool images and pushes as '-stage' tagged images to Docker Hub - build_containers_release.yml: triggers on release creation, builds all 7 tool images and pushes production images tagged with release version Both workflows use a matrix strategy across tools (blast, bwa, picard, quast, samtools, skesa, trimmomatic) and build for linux/amd64. Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Claude <noreply@anthropic.com>
- build_containers_stage.yml: manual workflow_dispatch trigger, builds all 7 tool images and pushes as '-stage' tagged images to Docker Hub - build_containers_release.yml: triggers on release creation, builds all 7 tool images and pushes production images tagged with release version Both workflows use a matrix strategy across tools (blast, bwa, picard, quast, samtools, skesa, trimmomatic) and build for linux/amd64. Co-Authored-By: Claude <noreply@anthropic.com>
…NIFEST.in - Move artwork/ and unique_references/ into microSALT/ package directory - Replace $CONDA_PREFIX/get_path expec path lookup with importlib.resources - Declare artwork/* and unique_references/* in pyproject.toml package-data - Update .gitignore BLAST index pattern to new path - Remove setup.py (data_files no longer needed) and MANIFEST.in Co-Authored-By: Claude <noreply@anthropic.com>
rannick
reviewed
Mar 20, 2026
rannick
reviewed
Mar 20, 2026
rannick
reviewed
Mar 20, 2026
rannick
reviewed
Mar 20, 2026
rannick
reviewed
Mar 20, 2026
rannick
reviewed
Mar 20, 2026
…ownloaded organisms
…pdate Stop updating references when using pipeline
rannick
reviewed
Mar 23, 2026
rannick
reviewed
Mar 23, 2026
….py and add ProfileCreationError exception
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
closes #241
This is a major update to microSALT doing the following:
Primary function of PR
Testing
bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAMEusconda activate S_microSALTmicroSALT analyse --input /path/to/fastq/ SAMPLEINFO_FILETest results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
Sign-offs