added sample irida_next sample field option #140
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
|
|
If these tests pass, a sample with the name |
kylacochrane
approved these changes
Oct 31, 2024
There was a problem hiding this comment.
Great work Matthew 😸
I don’t have any specific comments - this sample_name solution looks solid to me. I tried adding a helper function to simplify the inx_string_suffix extraction logic in updated_samples within main.nf, but it ended up making things more complicated than expected, haha!
apetkau
requested changes
Oct 31, 2024
sgsutcliffe
reviewed
Nov 1, 2024
sgsutcliffe
requested changes
Nov 4, 2024
There was a problem hiding this comment.
Following up on my comment, there needs to be a renaming of meta.id with meta.external_id when no sample_name is provided because it becomes null and then wants to group everything in the COMBINE_DATA() process. I tried using the map{} we have used in other pipelines but it wasn't working. I can give it more of a try.
What I tried doing was:
// Track processed IDs
def processedIDs = [] as Set
input = Channel.fromSamplesheet("input")
// and remove non-alphanumeric characters in sample_names (meta.id), whilst also correcting for duplicate sample_names (meta.id)
.map { meta ->
if (!meta.id) {
meta.id = meta.external_id
} else {
// Non-alphanumeric characters (excluding _,-,.) will be replaced with "_"
meta.id = meta.id.replaceAll(/[^A-Za-z0-9_.\-]/, '_')
}
// Ensure ID is unique by appending meta.external_id if needed
while (processedIDs.contains(meta.id)) {
meta.id = "${meta.id}_${meta.external_id}"
}
// Add the ID to the set of processed IDs
processedIDs << meta.id
tuple(meta)}.view()
in the input_check subworkflow but it tells me it cannot perform replaceAll because it is an ArrayList type.
|
One last comment! I promise, and a suggestion. Could we use |
sgsutcliffe
reviewed
Nov 8, 2024
apetkau
requested changes
Nov 8, 2024
There was a problem hiding this comment.
This looks great. Thanks so much for all your work @mattheww95 . A few inline comments.
sgsutcliffe
reviewed
Nov 8, 2024
sgsutcliffe
reviewed
Nov 8, 2024
sgsutcliffe
approved these changes
Nov 18, 2024
apetkau
approved these changes
Nov 25, 2024
There was a problem hiding this comment.
Thanks so much Matthew Wells for the amazing work you've done with this. And thanks so much Steven Sutcliffe for all your help reviewing 😄
I have tested this out in IRIDA Next starting from both assemblies. The output files are named properly, they are stored properly with the respective sample records, and metadata is written properly.
This all looks great. Approving this PR. I only made note of 2 small typos/fixes to text in-line to change.
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.
Added support for the irida_next sample id.