#2041 Add comment[file uri] column to PXD009752.sdrf.tsv Pull request opened by jonasscheid Summary Adds a

comment[file uri]

column to

testdata/PXD009752.sdrf.tsv

so the SDRF can be consumed by

sdrf-pipelines convert-openms

. The OpenMS converter does a hard pandas lookup on

comment[file uri]

(sdrf-pipelines

converters/openms/openms.py

); without the column it raises

KeyError

. 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.raw>

Why 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.tsv

succeeds locally (bioconda sdrf-pipelines 0.1.3) • mhcquant pipeline tests still pass with the modified SDRF (column is additive, mhcquant doesn't read it) nf-core/test-datasets