launch_example.sh 867 Bytes
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#!/bin/bash

sbatch -W -p workq -J functional_test --mem=6G \
	--wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq <metagwgs-src>/main.nf --step '01_clean_qc,02_assembly,03_filtering,04_structural_annot,05_alignment,06_func_annot,07_taxo_affi' --reads 'metagwgs-test-datasets-small/input/*_{R1,R2}.fastq.gz' --host_fasta 'metagwgs-test-datasets-small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_bwa_index 'metagwgs-test-datasets-small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --min_contigs_cpm 1000 --kaiju_db_dir '<bank>/kaijudb_refseq_2020-05-25' --taxonomy_dir '<bank>/taxonomy' --eggnog_mapper_db_dir '<bank>/eggnog-mapper-2.0.4-rf1/data' --diamond_bank '<bank>/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd' -with-report -with-timeline -with-trace -with-dag"