Changed Cutadapt to use nf-core modules #1335

Job	Run time
Test SISPA workflow (--gff false)	14m 37s
Test workflow parameters (--consensus_caller ivar)	4m 45s
Test SISPA workflow (--genome 'NC_045512.2')	14m 19s
Run pipeline with test data (23.04.0)	23m 21s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	4m 49s
Run pipeline with test data (latest-everything)	25m 25s
Test workflow parameters (--skip_fastp --skip_pangolin)	4m 44s
Test workflow parameters (--skip_variants)	4m 44s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	4m 42s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	24m 43s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	25m 35s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	24m 53s
Test workflow parameters (--skip_kraken2)	4m 27s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 29s
Test workflow parameters (--skip_assembly)	4m 43s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 20s
Test workflow parameters (--spades_mode corona)	4m 45s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	30m 58s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	30m 58s
Test workflow parameters (--spades_mode metaviral)	4m 44s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	4m 45s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	4m 46s
	4h 31m 32s

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