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"
}
}