Keep mgp_info in json

[aghozlane]

These information are included in mgp_info tag: { "sample_info": { "sample_name": "FG_1001461", "project_name": "french_gut", "host": "human", "scientific_name": "human gut metagenome", "taxon_id": "408070", "host body site": "human-gut", "backup_host_reads": "nosave", "run_name": "V350196990V350058381", "multi_project_chip": "0", "full_sample_name": "V350196990V350058381_L01_104_1", "read_length": "-1", "read_length_type": "variable", "sequencing_device": "DNBSEQ", "sequencing_model_device": "DNBSEQ-G400", "sequencing_device_internal_name": "R13040100200021", "center_name": "INRA-META", "library_type": "PE150", "lane": "L01", "tag": "1", "explicit_tag": "forward", "quality_encoding": "Phred+33", "sequencing_date": "2023-11-01", "sequenced_raw_read_count": "7542655", "host_read_count": "15142", "low_quality_read_count": "87227", "sequenced_read_count": "7440286" }, "sample_file": { "fastq_file": "V350196990V350058381_L01_104_1.clean.rmHost.fastq.gz", "raw_fastq_file": "V350196990V350058381_L01_104_1.fq.gz", "is_compressed": "1" }, "experiment": { "library_strategy": "WGS", "library_source": "METAGENOMIC", "library_selection": "RANDOM", "library_layout": "PAIRED", "library_construction_protocol": "Standard DNBSEQ-G400 protocol", "platform": "DNBSEQ", "instrument_model": "DNBSEQ-G400", "insert_size": "-1", "insert_size_sd": "-1" }, "trimming_general": { "username": "npons", "start_time": "2024-01-10T20:42:00.652265", "end_time": "2024-01-10T21:39:33.424428" }, "trimming_proactive_workflow": { "workflow_name": "fastp", "workflow_version": "0947dffd8c3861d4747cde3b08a5bece", "input_dir": "/scratch_global/npons/preprod_dnbseqdeployer/scratch/V350196990V350058381/french_gut/sample_raw", "output_dir": "/scratch_global/npons/preprod_dnbseqdeployer/scratch/V350196990V350058381/french_gut/sample_fastp", "forward_reads_suffix": "_1", "reverse_reads_suffix": "_2", "sequencing_adapters": "DNBseq", "keep_singletons": "False", "compress_output": "True" }, "trimming_fastp": { "version": "0.23.2", "parameters": "--cut_front --cut_tail --n_base_limit 0 --length_required 60 --adapter_sequence AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA --adapter_sequence_r2 AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG" }, "host_removing_general": { "username": "npons", "start_time": "2024-01-11T04:21:08.917997", "end_time": "2024-01-11T10:07:46.627461" }, "host_removing_proactive_workflow": { "workflow_name": "remove_host", "workflow_version": "b0deac2de0da4de9378a4ce663538d48", "input_dir": "/scratch_global/npons/preprod_dnbseqdeployer/scratch/V350196990V350058381/french_gut/sample_fastp", "output_dir": "/scratch_global/npons/preprod_dnbseqdeployer/scratch/V350196990V350058381/french_gut/sample_fastp_no_host", "forward_reads_suffix": "_1", "reverse_reads_suffix": "_2", "compress_output": "True" }, "host_removing_bowtie2": { "version": "2.5.1", "host_index": "/biodatabank/meteor-data/reference.ng/Homo_sapiens_chm13_t2t_v2/fasta/Homo_sapiens_chm13_t2t_v2_dnaspace_index", "alignment_parameters": "default" }, "host_removing_samtools": { "version": "1.9" } }