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new list of proteomics modules

Open rolivella opened this issue 1 year ago • 13 comments

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

rolivella avatar May 14 '24 08:05 rolivella

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 🙂

mirpedrol avatar May 14 '24 09:05 mirpedrol

Nice! I already started with a couple of openms tools that we use: https://github.com/nf-core/mhcquant/issues/296

jonasscheid avatar Sep 11 '24 06:09 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 avatar Sep 11 '24 06:09 jonasscheid

btw peptideindexer already exists: https://github.com/nf-core/modules/issues/4642

jonasscheid avatar Sep 11 '24 06:09 jonasscheid

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

rolivella avatar Sep 12 '24 12:09 rolivella

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

jonasscheid avatar Sep 13 '24 07:09 jonasscheid

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

jonasscheid avatar Sep 13 '24 07:09 jonasscheid

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

rolivella avatar Sep 13 '24 09:09 rolivella

@jonasscheid maybe you could be interested in this discussion: https://github.com/gtluu/timsconvert/issues/64

rolivella avatar Oct 07 '24 10:10 rolivella