new list of proteomics modules

[rolivella]

DDA

Process name	Link to quantms local module	Call	Tool	Test data	Test data (chunked)
cdecoy_pr	NA	create_decoy	decoy.pl	sp_human_2024_02.fasta_decoy.fasta
comet_adapter_pr	NA	CometAdapter	openms container	2022MQ777_DDA_TEST_01.raw.mzML
idfilter_pr	idfilter	NA	NA	2022MQ777_DDA_TEST_01.raw_comet.idXML
pepidx_pr	indexpeptides	NA	NA	2022MQ777_DDA_TEST_01.raw_comet_idfilter_aaa.idXML
fdr_pr	falsediscoveryrate	NA	NA	2022MQ777_DDA_TEST_01.raw_comet_idfilter_aaa_peptideindexer.idXML
fileinfo_pr	NA	FileInfo	openms container	2022MQ777_DDA_TEST_01.raw_comet_idfilter_aaa_peptideindexer_fdr_idfilter_score.idXML
protinf_pr	proteininference	NA	NA	2022MQ777_DDA_TEST_01.raw_comet_idfilter_aaa_peptideindexer_fdr_idfilter_score.idXML
ffm_pr	NA	FeatureFinderMultiplex	openms container	2022MQ777_DDA_TEST_01.raw.mzML
idmapper_pr	idmapper	NA	NA	2022MQ777_DDA_TEST_01.raw_ffm.featureXML
protquant_pr	NA	ProteinQuantifier	openms container	2022MQ777_DDA_TEST_01.raw_ffm_idmapper.featureXML
diann_pr	diann_preliminary_analysis	NA	NA	2022MK777_DIA_TEST_01.raw.mzML
mao_pr	NA	MascotAdapterOnline	openms container	2022MQ777_DDA_TEST_01.raw.mzML
timsconvert	NA	Usage	Install on linux	T061519_QC03_AurEl7_PM5_RA7_1_7694.d.zip
insertPolymerContToQSample_pr	NA	insertPolymerContToQSample	Install on Linux	2022MQ777_DDA_TEST_01.raw.mzML

[mirpedrol]

This issue tracks the proteomics modules that should be added to nf-core.

Some of them are available as local modules from the quantms pipeline, which have to be converted to nf-core modules.
For the rest of the modules we link the tool, if the container is available and test data.

Contributors are welcome 🙂

[jonasscheid]

Nice! I already started with a couple of openms tools that we use: nf-core/mhcquant#296

[jonasscheid]

@rolivella bruker recommends to use tdf2mzml for parsing .d -> mzML. Might be worth to focus on that tool, there is also an existing docker container on dockerhub

[jonasscheid]

btw peptideindexer already exists: #4642

[rolivella]

@jonasscheid ok! we can start with this bruker conversor. Where is the container?

[jonasscheid]

Module ref: https://github.com/nf-core/mhcquant/blob/master/modules/local/tdf2mzml.nf

[jonasscheid]

@rolivella Do you have experience with timsconvert? :) Out of curiosity

[rolivella]

No, I'm afraid I don't have any experience...

[rolivella]

@jonasscheid maybe you could be interested in this discussion: gtluu/timsconvert#64