Repository navigation
Conversation
The shipped test flowcell is a 1-lane run (RunInfo.xml LaneCount=1, SampleSheet.csv declares only lane 1), but the seed document declared all 8 lanes of the NextSeq 2000. Downstream consumers that plan per lane (e.g. the demux realm in dataflow_testing) then plan and fail lane 2-8 branches that have no data on disk.
The seed said Y151;N10;N10;Y151 (4 reads) but the shipped test flowcell's RunInfo.xml declares two 151-cycle reads (its own SampleSheet.csv says Y151;Y151), so bcl-convert rejected the rendered samplesheet with 'The number of reads specified in OverrideCycles must match the number of reads in the RunInfo.xml'.
Contributor
|
Is it something that makes sense in the mid-/long-term? Meaning, does this branch need merging or is it just for testing until we figure out why it does not work with the additional lanes? We can strip them away, but since the real data on StatusDB look like this, it will then fail in "production". |
Member
Author
|
This is mainly for testing yes. We can leave this as PR and you can have a stab at running the demux with demux realm. I believe bclconvert was complaining for all the other lanes due to the RunInfo.xml file that I had. So its definitely possible to fix in the training data rather than cutting off all other lanes here. |
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
To get demultiplexing to work inside dataflow_testing qwen wanted to strip out all lanes but the first one.