### docs/plans/20260526T224018Z_blahab44_inputs/ont_hg003_5x.tsv
RUN_ID	SAMPLE_ID	EXPERIMENTID	SAMPLESOURCE	SAMPLECLASS	BIOLOGICAL_SEX	SAMPLE_TYPE	LIB_PREP	SEQ_VENDOR	SEQ_PLATFORM	LANE	SEQBC_ID	PATH_TO_CONCORDANCE_DATA_DIR	CONCORDANCE_CONTROL_PATH	TRUTH_DATA_DIR	R1_FQ	R2_FQ	ILMN_R1_FQ	ILMN_R2_FQ	CG_R1_FQ	CG_R2_FQ	PACBIO_R1_FQ	PACBIO_R2_FQ	ONT_R1_FQ	ONT_R2_FQ	ONT_FASTQ_PREFIX	ONT_FLOWCELL_ID	UG_R1_FQ	UG_R2_FQ	ULTIMA_CRAM	ULTIMA_CRAM_ALIGNER	ULTIMA_CRAM_SNV_CALLER	ULTIMA_SUBSAMPLE_PCT	ONT_CRAM	ONT_CRAM_ALIGNER	ONT_CRAM_SNV_CALLER	ONT_SUBSAMPLE_PCT	PB_BAM	PB_BAM_ALIGNER	PB_BAM_SNV_CALLER	ONT_BAM	ONT_BAM_ALIGNER	ONT_BAM_SNV_CALLER	ROCHE_BAM	ROCHE_BAM_ALIGNER	ROCHE_BAM_SNV_CALLER	ROCHE_DOWNSAMPLE_RATIO	STAGE_DIRECTIVE	STAGE_TARGET	SUBSAMPLE_PCT	ILMN_TRIM_READ_LENGTH	LONGREADTRIM_READ_LENGTH	LONGREADTRIM_MODE	SAMPLEUSE	BWA_KMER	DEEP_MODEL	IS_POS_CTRL	IS_NEG_CTRL	TUM_NRM_SAMPLEID_MATCH	N_X	N_Y	EXTERNAL_SAMPLE_ID
TVBONT5X	HG003	5x	blood	research	male	gdna	PF	ONT	PROMETHION	1	D0	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/																			/fsx/references/genomic_data/organism_reads_slim/cram/H_sapiens/giab/agbt_2026/ont/HG003_5x.cleaned.cram	ont	sentdont												pass_through	/fsx/staging/staged_external_sequencing_data	na				posControl	19	ONT_R104	true	false	na	1	1	HG003
### docs/plans/20260526T224018Z_blahab44_inputs/illumina_hg003_5x.tsv
RUN_ID	SAMPLE_ID	EXPERIMENTID	SAMPLESOURCE	SAMPLECLASS	BIOLOGICAL_SEX	SAMPLE_TYPE	LIB_PREP	SEQ_VENDOR	SEQ_PLATFORM	LANE	SEQBC_ID	PATH_TO_CONCORDANCE_DATA_DIR	CONCORDANCE_CONTROL_PATH	TRUTH_DATA_DIR	R1_FQ	R2_FQ	ILMN_R1_FQ	ILMN_R2_FQ	CG_R1_FQ	CG_R2_FQ	PACBIO_R1_FQ	PACBIO_R2_FQ	ONT_R1_FQ	ONT_R2_FQ	ONT_FASTQ_PREFIX	ONT_FLOWCELL_ID	UG_R1_FQ	UG_R2_FQ	ULTIMA_CRAM	ULTIMA_CRAM_ALIGNER	ULTIMA_CRAM_SNV_CALLER	ULTIMA_SUBSAMPLE_PCT	ONT_CRAM	ONT_CRAM_ALIGNER	ONT_CRAM_SNV_CALLER	ONT_SUBSAMPLE_PCT	PB_BAM	PB_BAM_ALIGNER	PB_BAM_SNV_CALLER	ONT_BAM	ONT_BAM_ALIGNER	ONT_BAM_SNV_CALLER	ROCHE_BAM	ROCHE_BAM_ALIGNER	ROCHE_BAM_SNV_CALLER	ROCHE_DOWNSAMPLE_RATIO	STAGE_DIRECTIVE	STAGE_TARGET	SUBSAMPLE_PCT	ILMN_TRIM_READ_LENGTH	LONGREADTRIM_READ_LENGTH	LONGREADTRIM_MODE	SAMPLEUSE	BWA_KMER	DEEP_MODEL	IS_POS_CTRL	IS_NEG_CTRL	TUM_NRM_SAMPLEID_MATCH	N_X	N_Y	EXTERNAL_SAMPLE_ID
TVBILMN5X	HG003	5x	blood	research	male	gdna	PF	ILMN	NOVASEQ	1	D0	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/			/fsx/references/genomic_data/organism_reads_slim/fastq/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_5x_R1.fastq.gz	/fsx/references/genomic_data/organism_reads_slim/fastq/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_5x_R2.fastq.gz																													pass_through	/fsx/staging/staged_external_sequencing_data	na				posControl	19	WGS	true	false	na	1	1	HG003
### tmp/live-validation/johnm_hg002_multifq_fix_20260519T133147Z/analysis_samples.hg002_multifq.tsv
RUN_ID	SAMPLE_ID	EXPERIMENTID	SAMPLE_TYPE	LIB_PREP	SEQ_VENDOR	SEQ_PLATFORM	LANE	SEQBC_ID	PATH_TO_CONCORDANCE_DATA_DIR	ILMN_R1_FQ	ILMN_R2_FQ	STAGE_DIRECTIVE	STAGE_TARGET	SUBSAMPLE_PCT	SAMPLEUSE	BWA_KMER	DEEP_MODEL	IS_POS_CTRL	IS_NEG_CTRL	N_X	N_Y	EXTERNAL_SAMPLE_ID
GIAB-HG002-multifq	HG002	split1x	blood	PCR-FREE	ILMN	NOVASEQX	0	S1	/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/	s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L001_R1.fastq.gz,s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L002_R1.fastq.gz,s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L003_R1.fastq.gz	s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L001_R2.fastq.gz,s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L002_R2.fastq.gz,s3://lsmc-dayoa-omics-analysis-us-west-2/data/staged_sample_data/multifq_hg002_split_20260519T132152Z/HG002_1x_L003_R2.fastq.gz	stage_data	/data/staged_sample_data	na	sample	19	WGS	false	false	1	1	HG002
