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nf-core / modules

Repository to host tool-specific module files for the Nextflow DSL2 community!
https://nf-co.re/modules
MIT License
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new list of proteomics modules #5599

Open rolivella opened 2 months ago

rolivella commented 2 months ago

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 commented 2 months ago

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 🙂