1.1.0 Updates #42
Open
1.1.0 Updates #42
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
Updating dev versions to 1.1.0dev
…all na values are correctly set to 0
1.1.0 Updates
…run on just the genome, jsut the transcriptome, or both
Add in oarfish as additional quantification method
|
|
@atrull314 : one thing I did just now catch is that we should disable |
itrujnara
reviewed
Jan 8, 2025
| ext.args = { | ||
| [ | ||
| "--threads 30", | ||
| params.barcode_format == "10X_3v3" ? "--kit-version 3v3" : params.barcode_format == "10X_5v2" ? "--kit-version 5v2" : "" |
There was a problem hiding this comment.
Is this information not required anymore?
There was a problem hiding this comment.
Correct, we had modified the blaze module to base threads off task.cpus as is the case with other modules, which resulted in this piece of the documentation being invalidated. This specific change was to resolve an error in documentation that we had put in before the change to the blaze module.
modules/local/merge_mtx.nf
Outdated
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' |
There was a problem hiding this comment.
Should be resolved with commit 57258d7
| "${task.process}": | ||
| python: \$(python --version | sed 's/Python //g') | ||
| END_VERSIONS | ||
| """ |
There was a problem hiding this comment.
Consider adding a stub, might be handy later
There was a problem hiding this comment.
Should be resolved with commit 57258d7
| "${task.process}": | ||
| oarfish: \$(oarfish --version | sed 's#oarfish ##g') | ||
| END_VERSIONS | ||
| """ |
There was a problem hiding this comment.
Should be resolved with commit 57258d7
| def args = task.ext.args ?: '' | ||
|
|
||
| """ | ||
| awk '/^>/{chrom=(split(substr(\$0,2), a, " ")); filename=( a[1] ".split.fa"); print > filename; next}{print >> filename}' $fasta |
There was a problem hiding this comment.
Does this have to be a new module? Looks like the same result could be achieved with the gawk nf-core module
There was a problem hiding this comment.
So the issue is the gawk nf-core module outputs as a single file, this awk statement is splitting a fasta into all of the chromosomes that compose it, so we need all the individual chromosome fastas as outputs. I'm not sure the module currently supports this behavior
|
|
||
| ch_gene_qc_stats = Channel.empty() | ||
| ch_transcript_qc_stats = Channel.empty() | ||
| if (quantifier.equals("oarfish")) { |
There was a problem hiding this comment.
Is the "both" option handled correctly here?
There was a problem hiding this comment.
Yep! Its handled in a separate file to make sure they are able to run in parallel.
| ch_transcript_qc_stats = QUANTIFY_SCRNA_ISOQUANT.out.transcript_qc_stats | ||
| } | ||
|
|
||
| emit: |
There was a problem hiding this comment.
Should be resolved with commit 6c6e7ec
| // | ||
| // MODULE: Samtools Merge | ||
| // | ||
| SAMTOOLS_MERGE ( |
There was a problem hiding this comment.
Should be resolved with commit 67d0ab3
| // | ||
| // MODULE: Samtools Index | ||
| // | ||
| SAMTOOLS_INDEX_MERGED( ch_dedup_single_bam ) |
There was a problem hiding this comment.
Should be resolved with commit 67d0ab3
| validate_params, | ||
| "nextflow_schema.json" | ||
| null |
There was a problem hiding this comment.
I think this may have been a merge issue, but should be resolved with commit 9951f69
@itrujnara I think I have resolved all your points, please resolve them as you see fit or we can discuss alternative solutions. Thanks! |
itrujnara
approved these changes
Jan 15, 2025
lianov
requested changes
Jan 15, 2025
| params.skip_bam_nanocomp, | ||
| params.skip_seurat, | ||
| false, | ||
| false |
There was a problem hiding this comment.
Disabling splitting the BAM in the transcriptomic data is currently creating a bottleneck at this step in regards to run time (BAM deduplication). This was originally solved in the genome mapping by splitting the BAM by chromosome, but due to the nature of the transcriptomic mappings, this cannot be enabled at this step as is.
@atrull314 and I are currently evaluating different approaches to implementing this optimization (or an alternative method), and once we have updated this portion of the workflow, the PR can move forward.
Hi @itrujnara, As @lianov mentioned we actually ended up finding an issue while we were performing validation of results that resulted in increased runtimes for our deduplication steps. I've kept the PR with the new changes so its easier to review, its available here #43. If you wouldn't mind taking a look when you have a chance. Thanks, |
|
@itrujnara : yes just adding a note here, that I the PR #43 is now approved but that we have not merged into dev yet as reviewing any other changes in that PR would likely be easier. It is all good from my end, and once it makes it to the dev branch and I can approve this one. |
|
Hi @itrujnara, Just wanted to reach out again and ask if you wouldn't mind taking a look at PR #43 for the review. Thanks, |
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.
PR Checklist
This PR contains the following updates for v1.1.0 of the pipeline: