This repository has been archived by the owner on Apr 19, 2023. It is now read-only.
Feature/255 freemuxlet generic inputs #330
Merged
Conversation
This file contains 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
- backwards-compatible change to add optional barcode_tag param - aertslab/popscle_helper_tools/issues/6
- Separate functions to take in data from getDataChannel and get the bam and barcodes files for the cellranger-style data - For bam,tsv input, join these dataChannels together on sampleId - Automatically handle multiple input types from getDataChannel and these can be run simultaneously - Resolves #255
Merged
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
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Outdated suggestions cannot be applied.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.
This allows multiple input formats for popscle (freemuxlet/demuxlet).
When using the
getDataChannelmethod to import data (specified with e.g.-profile cellranger_mex), thedata_channel_to_bam_barcodesfunction is used, and can format any of the cellranger channels to a tuple of(sampleId, bam, barcodes.tsv).Input with a (non-cellranger) bam and barcodes.tsv is possible by using
-profile bam,tsv. Here, the bam and tsv channels are joined on the sampleId key. A new parameterbarcode_tagallows specification of a different tag than the defaultCB.When using a workflow that first runs cellranger, the cellranger outputs don't include the full set of values that
getDataChannelproduces (type, format, group), but these can be assumed and handled by theget_bam_barcodes_from_cellranger_[rna|atac|arc]functions.