OpenMS parsing

[enryH]

First of all thanks for the great tool. I use it within the nextflow pipelinebigbio/quantms and try to analyze the ProteoBench DDA ion quant module. Therefore I subselected the relevant rows from the SDRF file provide along side PXD028735. The file is the following.

dda_lfq_proteobench_SDRF.sdrf.txt

If I parse this for openms as describe in the latest nfcore workflow step:

https://github.com/bigbio/quantms/blob/655b159251206d862039d8e3990558607355c62b/modules/local/sdrfparsing/main.nf

so translated for the example this would be

parse_sdrf convert-openms -t2 -l  --extension_convert raw:mzML -s dda_lfq_proteobench_SDRF.sdrf.txt

However for OpenMS ProteomicsLFQ this produces an invalid experimental design file. The concentration duplicates for the mixture of samples are not reduced leading to a an error saying ((Fraction Group, Fraction, Label) combination can only appear once), whos combination are indeed not unique.

Fraction_Group	Fraction	Spectra_Filepath	Label	Sample
1	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML	1	1
1	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML	1	1
1	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML	1	1
2	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML	1	2
2	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML	1	2
2	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML	1	2
3	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML	1	3
3	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML	1	3
3	1	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML	1	3
4	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML	1	4
4	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML	1	4
4	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML	1	4
5	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML	1	5
5	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML	1	5
5	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML	1	5
6	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML	1	6
6	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML	1	6
6	1	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML	1	6

Sample	MSstats_Condition	MSstats_BioReplicate
1	cond_A	1
2	cond_A	2
3	cond_A	3
4	cond_B	4
5	cond_B	5
6	cond_B	6

instead of

Fraction_Group	Fraction	Spectra_Filepath	Label	Sample
1	3	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML	1	1
2	3	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML	1	2
3	3	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML	1	3
4	3	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML	1	4
5	3	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML	1	5
6	3	LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML	1	6

Sample	MSstats_Condition	MSstats_BioReplicate
1	cond_A	1
2	cond_A	2
3	cond_A	3
4	cond_B	4
5	cond_B	5
6	cond_B	6

I can fix it manueally by removing duplicated raw file entries from the SDRF file, but I wonder if this should be handled better?