; ==== CORE-NT SFM MARCH 2026 UPDATE ==== ;

[GENERAL]
order = remove_adapters fastp_filter bowtie2_alignment downsample_nc15 filter_presence10 remove_taxids control_simple sam_sort_coord sam_index merge_refs filter_presence200 sam_sort_coord sam_index sam_sort_name
dry_run = False
threads = 32
input_manifest = "/eccs/home/pelibby16/research/skalanes-farm-mound/2026/manifest_sfm.csv
input_fastq_path = "/mounts/lovelace2/sequencer-output/Skalanes-farm-mound-2022-shotgun/fastq/"
output_path = "/mounts/lovelace/temporary/porter/SFM_coreNT_Mar2026"

[remove_adapters]
software = adapterremoval
args = --collapse --qualitybase 33 --qualitymax 41 --minadapteroverlap 5 --mm 3 --shift 2 --trimns --maxns 2 --trimqualities --minquality 15 --minlength 25 --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --interleaved-output 

[fastp_filter]
software = fastp
args = --dedup --low_complexity_filter --complexity_threshold 50 --length_required 35

[bowtie2_alignment]
software = bowtie2split
args = -x /mounts/lovelace2/indexes/ncbi/core_nt/bowtie2/ -q --phred33 --local --very-sensitive --no-unal -k 500 --mm --time --end-to-end --ramdisk /mounts/ramdisk/

; --very-sensitive = -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
; Handled internally: --rg-id --rg -S --threads --interleaved

[downsample_nc15]
software = downsample
args = --p 0.0560712594

[sam_sort_coord]
software = samtools
args = sort -O bam

[sam_sort_name]
software = samtools
args = sort -N -O bam

[sam_index]
software = samtools
args = index

[merge_refs]
software = mergebyhorizon
args =

[remove_taxids]
software = remove_taxids
args = -t 9903 -t 2157

[filter_presence10]
software = filterpresence
args = --presence_threshold 10

[filter_presence200]
software = filterpresence
args = --presence_threshold 200

[control_simple]
software = control_simple
args =

[pmd_analysis]
software = pmdtools
args = --threshold -5