Annotation_dev #9
Open
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
This adds some files to assets (to be ignored for now). They will eventually be used for annotating genes and generating web summaries. More importantly, this commit infers the species from the reference genome path and gets the associated genes.gtf file for velocyto to use.
Now, a matrix is
Using gene annotation matrices in assets, the data-matrix is annotated and stored in an AnnData object. It also calculates doublet scores for the matrix. If the reference genome is unsupported, it will just not annotate gene types, but still calculate doublets. RNA-velocity support to be added soon.
Gene annotations
This commit allows the pipeline to annotate annotate the filtered_feature_bc_matrix.h5 file outputted by 'cellranger'. It also allows for optional RNA velocity analysis with 'velocyto'.
This `Nextflow` script will now take `cellranger count` outputs and generate `AnnData` and `Seurat` objects. They are annotated with various QC statistics as well as gene types. The pipeline also generates plots of the QC statistics, while generating an `HTML` document that summarizes the pipeline's outputs. This `HTML` summary is incomplete at the moment and likely to change a lot as the outputs are organized.
|
Commit |
ahmed-said-jax
commented
May 3, 2023
src/create_gene_annotations.py
Outdated
|
|
||
| # The two currently supported species have different file types | ||
| # and formats, so they need to be handled differently | ||
| if ds == "hsapiens_gene_ensembl": |
There was a problem hiding this comment.
this branching behavior feels ugly to me but i don't have a better solution at the moment
This commit creates a nearly fully functional annotation pipeline. After `cellranger count` creates a `filtered_feature_bc_matrix`, `soupx` creates its own from the `cellranger` outputs. The `soupx` matrix should have ambient RNA filtered out. Both matrices are then annotated in parallel for various gene types and doublets, and plots are generated automatically, as well as a web summary including plots. The web summary is as of yet incomplete, as it does not contain a list of the genes annotated, nor does it create the correct directory tree. The flowchart is also incorrect at the moment.
ahmed-said-jax
commented
May 4, 2023
ahmed-said-jax
commented
May 10, 2023
ahmed-said-jax
commented
May 12, 2023
modules/gen_info.nf
Outdated
| script: | ||
| """ | ||
| gen_plots.py | ||
| gen_summary.py --summary_dir=${summary_dir} --pubdir=${launchDir / params.pubdir} |
There was a problem hiding this comment.
the pubdir here might need to be changed
The pre-analysis (annotation) pipeline now works as expected and produces an HTML summary with correct information. It also now has a table of annotated genes.
This commit updates the README to contain information about pre-analysis gene/cell annotation for single cell expression. Additionally, it updates `tools.csv` to contain the correct doublet detection algorithm. Finally, it updates `annotate.py` to make it case-insensitive for Ensembl gene IDs in the reference annotations, in case a user passes in their own files with lowercased gene IDs.
wflynny
requested changes
May 30, 2023
modules/ambient_rna.nf
Outdated
|
|
||
| script: | ||
| """ | ||
| mimic_cellranger.py --soupx_dir=${tool} |
There was a problem hiding this comment.
Can the functionality of mimic_cellranger.py be accomplished via bash cp commands and changing how inputs are staged?
There was a problem hiding this comment.
i think this is probably the simplest way to do it, but is this safe? in particular, the rm -r step scares me
ahmed-said-jax
commented
May 30, 2023
| @@ -14,15 +14,21 @@ nextflow.enable.dsl = 2 | |||
|
|
|||
| params.pubdir = params.getOrDefault("pubdir", "pubdir") | |||
There was a problem hiding this comment.
is the getOrDefault thing necessary? can't we just do params.thing = 'value' for the same effect?
Suggested change
| params.pubdir = params.getOrDefault("pubdir", "pubdir") | |
| params.pubdir = "pubdir" |
There was a problem hiding this comment.
and i mean that for all the parameters, not just the pubdir
Simplified pipeline and make plotting more robust.
…etries in elion profile
Remove `**/*test*` from `.gitignore`
The container is now set to pull from the remote container registry.
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.
This commit allows the pipeline to annotate
the filtered_feature_bc_matrix.h5
file outputted by
cellranger. It also allowsfor optional RNA velocity analysis with
velocyto.