Error while running with OpenMS experimental design format

[EfraMP]

Hi,

Thank you for your hard work. This is an interesting project. When I was trying to test the pipeline with a custom TSV following the OpenMS experimental design format I got the next error:

Command output:
  the one-table format parser is broken in OpenMS2.5, please use one-table or sdrf

Is there an easy solution to this? Thanks in advance!

[daichengxin]

Could you share your OpenMS experimental design format? A reference format is here https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv

[EfraMP]

Sure.

This is the TSV file:

Fraction_Group	Fraction	Spectra_Filepath	Label	MSstats_Condition	MSstats_BioReplicate
1	1	/path/to/mzML/file/TECANuno_2ulMM_rep1_R1.mzML	1	2ulMM	1
2	1	/path/to/mzML/file/TECANuno_2ulMM_rep2_R1.mzML	1	2ulMM	2
3	1	/path/to/mzML/file/TECANuno_2ulMM_rep3_R1.mzML	1	2ulMM	3
4	1	/path/to/mzML/file/TECANuno_4ulMM_rep1_R1.mzML	1	4ulMM	1
5	1	/path/to/mzML/file/TECANuno_4ulMM_rep2_R1.mzML	1	4ulMM	2
6	1	/path/to/mzML/file/TECANuno_4ulMM_rep3_R1.mzML	1	4ulMM	3

And this is the command I used:

⁠ nextflow run bigbio/quantms --input /path/to//file/quantms_input.tsv --database /path/to/fasta/file.fasta --outdir './results' -profile docker --acquisition_method dia --labelling_type 'label free sample' --enable_pmultiqc ⁠