FloRes/params_google_batch.yaml at master · passdan/FloRes · GitHub

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pipeline: "demo"
reads: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/raw/*_R{1,2}.fastq.gz"
bam_files: null
split: ""

host: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/host/chr21.fasta.gz"
host_index: null
kraken_db: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/kraken_db/minikraken_8GB_20200312"
amr_index: null
amr: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/amr/megares_database_v3.fasta"
annotation: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/amr/megares_annotations_v3.00.csv"

output: "gs://nf-vwb-dev-beaming-hazelnut-6046/results"

snp: "N"
deduped: "N"
prefix: "AMR"
threads: 8

adapters: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/adapters/nextera.fa"
leading: 3
trailing: 3
slidingwindow: "4:15"
minlen: 36

threshold: 80
min: 5
max: 100
skip: 5
samples: 1

multiqc: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/multiqc"
p_trim_left_f: 25
p_trim_left_r: 26
p_trunc_len_f: 225
p_trunc_len_r: 220

taxlevel: "R1,R2,R3,K,P,C,O,F,G,S"
dada2_db: "gs://nf-vwb-dev-beaming-hazelnut-6046/data/qiime/gg-13-8-99-515-806-nb-classifier.qza"