5. fastQSample or Output folder mode

To configure the pipeline to generate a brief output file for each request containing almost all the QC metrics:

1. In the output_folder field of the assets/defaultlab_methods.csv, specify the desired output directory, such as /home/atlas_output. That's all you need to do.
2. From this point onward, each request's results will be saved in the output_folder with filenames following the format request_code.tsv.
3. Each TSV file will contain almost all the metrics present on the QSample website.

TSV sample content:

filename	num_prots	num_peptd	miscleavages_0	miscleavages_1	miscleavages_2	miscleavages_3	charge_2	charge_3	charge_4	total_base_peak_intenisty	total_tic
2025MQ004_sample_001_01_1ug	136	648	574	73	2	0	574	337	37	4503904665188.7303658444095	22386273674914.6906373591452
2025MQ004_sample_003_01_1ug	175	782	607	165	11	0	641	454	104	8664404227869.0920296464814	43232622426793.3020685989287
2025MQ004_sample_002_01_1ug	144	678	615	63	1	0	601	344	38	3552646099051.2823144021850	18264810179972.6938288350508
2025MQ004_sample_004_01_1ug	78	380	358	23	0	0	328	159	25	1835341886132.3502026709201	10291655129272.7863353202465
2025MQ004_sample_001_02_1ug	205	917	777	138	3	0	845	454	52	3116870764252.1011810521215	14548693281706.188573989363
2025MQ004_sample_003_02_1ug	185	905	683	211	12	0	763	557	130	7271508336589.8163719338588	35566415809951.662882404699
2025MQ004_sample_002_02_1ug	207	987	814	172	2	0	900	492	54	2995786289007.2798042486470	13843645516575.784217466996
2025MQ004_sample_004_02_1ug	119	598	528	69	2	0	556	275	23	1068304805293.5685997257684	5265952526025.956108787555