Add comment[file uri] column to PXD009752.sdrf.tsv#2041
Merged
jonasscheid merged 1 commit intonf-core:mhcquantfrom May 8, 2026
Merged
Add comment[file uri] column to PXD009752.sdrf.tsv#2041jonasscheid merged 1 commit intonf-core:mhcquantfrom
jonasscheid merged 1 commit intonf-core:mhcquantfrom
Conversation
…elines convert-openms
mashehu
approved these changes
May 8, 2026
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
Adds a
comment[file uri]column totestdata/PXD009752.sdrf.tsvso the SDRF can be consumed bysdrf-pipelines convert-openms.The OpenMS converter does a hard pandas lookup on
comment[file uri](sdrf-pipelinesconverters/openms/openms.py); without the column it raisesKeyError. Other converters (mhcquant, msstats, normalyzerde, diann) tolerate the column being absent, so this change is purely additive for them.The added URI is the canonical PRIDE archive FTP location for the raw file:
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD009752/IP_lung_1T_060317_1.rawWhy
Unblocks a single shared SDRF for testing all
parse_sdrf convert-*subcommands in nf-core/modules#11514. Without this, the openms test in that PR has to fetch a different SDRF from upstream sdrf-pipelines (extra cross-test HTTP request).Test plan
parse_sdrf convert-openms -s testdata/PXD009752.sdrf.tsvsucceeds locally (bioconda sdrf-pipelines 0.1.3)