Add ability to specify entire read group tag in "info" field #295
Draft
pauldwolfe wants to merge 2 commits into
Draft
Add ability to specify entire read group tag in "info" field #295pauldwolfe wants to merge 2 commits into
pauldwolfe wants to merge 2 commits into
Conversation
In the sample sheet. This will give users complete control over the RG used in alignment, rather than needing to specify every field individually.
Replace the verbatim read group string with a |-delimited list of TAG=value SAM fields (e.g. read_group:ID=S1.L001|PL=ILLUMINA). The fields are stored aligner-agnostically and formatted per-aligner so the same syntax works for both BWA-MEM2 (DNA) and STAR (RNA), rather than requiring users to match each aligner's read group syntax. ID and SM default to the sample/library/lane identifiers and may be overridden. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Member
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Use a |-delimited list of TAG=value SAM fields (e.g. read_group:ID=S1.L001|PL=ILLUMINA). Thefields are stored aligner-agnostically and formatted per-aligner so the same syntax works for both BWA-MEM2 (DNA) and STAR (RNA), rather than
requiring users to match each aligner's read group syntax. ID and SM default to the sample/library/lane identifiers and may be overridden.