WARN: Access to undefined parameter `genome` -- Initialise it to a default value eg. `params.genome = some_value`
WARN: Access to undefined parameter `host_genomes` -- Initialise it to a default value eg. `params.host_genomes = some_value`
ERROR ~ Cannot invoke method keySet() on null object

 -- Check script '/cluster/home/thhaverk/.nextflow/assets/nf-core/mag/./subworkflows/local/utils_nfcore_mag_pipeline/main.nf' at line: 353 or see '.nextflow.log' file for more details

nextflow run nf-core/mag -r 3.2.1 -profile apptainer -work-dir $USERWORK/nf_mag -resume -params-file params.json

{
		"input": "samplesheet_large.csv",
		"outdir": "\/cluster\/projects\/nn10070k\/projects\/phagedrive\/pd_data_control\/results\/20241125_MAG_results",
		"multiqc_title": "MQC_FULL_SAMPLE_RUN",
		"reads_minlength": 50,
		"igenomes_base" : "s3://ngi-igenomes/igenomes",
		"gtdb_db": "\/cluster\/projects\/nn10070k\/databases\/gtdbtk_r220_data.tar.gz", 
		"host_genome": "GRCh38",
		"kraken2_db": "\/cluster\/projects\/nn10070k\/databases\/kraken2_pluspfp_05.06.2024\/hash.k2d",
		"cat_db": "\/cluster\/projects\/nn10070k\/databases\/20240422_CAT_nr",
		"binqc_tool": "checkm",
		"checkm_db": "\/cluster\/projects\/nn10070k\/databases\/checkm_db_2015.01.16",
		"busco_db": "\/cluster\/shared\/biobases\/BUSCO\/2024-11-21",
		"busco_auto_lineage_prok": true,
		"busco_clean": true,
		"run_gunc": true,
		"gunc_db": "\/cluster\/projects\/nn10070k\/databases\/gunc_db_progenomes2.1\/gunc_db_progenomes2.1.dmnd",
		"refine_bins_dastool": true,
		"postbinning_input": "refined_bins_only",
		"run_virus_identification": true	
	}