Make it work without specifying GTF file #322
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
|
fmalmeida
reviewed
May 1, 2024
Comment on lines
-31
to
-32
| ch_genome_fasta = params.genome ? file( getGenomeAttribute('fasta'), checkIfExists: true ) : [] | ||
| ch_gtf = params.genome ? file( getGenomeAttribute('gtf'), checkIfExists: true ) : [] |
There was a problem hiding this comment.
Was it required to be removed from the main.nf. Was it it the "main"-template functions that were complaining about not providing a fasta?
If that is the case, I would say this is a ticket that should be taken entirely at once, in a separate one, because it would affect all of the workflows.
Thus having a single issue to take a look at this matter for all workflows would be easier to track.
Issues that could be optionally merged together for it are: #313 and #277 .
There was a problem hiding this comment.
I think #313 is already part of the cellranger multi PR.
I wasn't aware that there's a linting check for that, but I'd argue that as it is currently implemented is suboptimal. Either
- all parameters should be evaluated outside the scrnaseq workflow and passed as arguments
- all parameters should be evaluated within the workflow and not arguments should be passed.
Currently it is just inconsistent with fastq/gtf being passed as arguments and to me it's highly confusing that different parts of the workflow partly evaluate some parameters. It also doesn't help because you anyway can't include the workflow somewhere else and run it as it is currently implemented.
For the sake of simplicitly I'd vote for sticking with what we currently have (i.e. evaluate parameters within the workflow) and if necessary ignore the respective linting checks. The solution intended by the template authors would probably be to move all parameter checks outside the workflow and pass them as arguments.
There was a problem hiding this comment.
linting doesn't seem to fail because of this btw.
There was a problem hiding this comment.
That is true, every other subworkflow currently, have the input assertion happening inside the sub-workflow itself:
e.g. alevin
assert (genome_fasta && gtf && salmon_index && txp2gene) || (genome_fasta && gtf) || (genome_fasta && gtf && transcript_fasta && txp2gene):
"""Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf'), or a genome fasta file
and a transcriptome fasta file ('--transcript_fasta`) if no index and txp2gene is given!""".stripIndent()However, they are indeed seeming to rely on gtf/fasta that had been file() loaded outside. So, we should also bring the loaders to the inside the sub-workflow on the others as well.
Is that the correct understanding?
There was a problem hiding this comment.
No, I think the subworkflows (for each aligner) should be fully abstracted (i.e. not rely on params anywhere, but just consume input channels/values via take).
It's just about whether to evaluate params in main.nf or in workflows/scrnaseq.nf.
There was a problem hiding this comment.
Ah!,
Now I can see it clearly that the changes were happening in these two.
For some reason I was reading as if they were included inside the cellrangermulti sub-workflow.
🤯
fmalmeida
approved these changes
May 2, 2024
fmalmeida
merged commit 5cdb691
into
247-support-for-10x-ffpe-scrna
11 of 12 checks passed
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.
Wanted to run cellranger multi with just specifying the cellranger index. Likely affected other workflows, too.