feat: add support for multi-lane samples
In the previous version, the workflow was working under the assumption that each sample name only appears once in the samples table. This was a bottleneck for incorporating multi-lane samples, as this led to multiple lines with the same sample (each line one lane with individual paths to fastq files). This is now dealt in the following way: same mate files with the same sample name are concatenated in the beginning and a function ensures that features that should be sample-dependent are not returned multiple times (due to the multiple-lines with same sample issue). Additionally, a separate test is created to test this functionality, with a samples table containing multi-lane samples.
Closes #115 (closed)
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Activity
changed milestone to %v0.2.0 release
added Testing & CI/CD + 1 deleted label
added 1 commit
- f3341553 - refactor: removed redunant file and code from test_integration_workflow_multiple_lanes
added 1 commit
- a6eb2ddb - fix: bug in test_workflow_multiple_lanes/test.slurm.sh calling config instead...
- Resolved by Alex Kanitz
It looks good to me and from my side I would merge after changing the merge request description (there's a comment there how/why) and opening one or two separate issues for fixing more general stuff that affects other code/tests as well. I can't really review the changes to the Snakemake pipeline though (and they are a lot), so would feel better if @gypas could have another pass over that.
- Last reply by Alex Kanitz
mentioned in commit ce1b6162
