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test.sh
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test.sh
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#!/bin/bash
set -e
# Run this script to test geneshot on the example data in the repository
# All execution will be done locally using Docker, so there is no need to
# set up HPC or cloud execution configurations
# 0. Make sure you have a working installation of Nextflow and Docker
# 1. Download or clone this repository
# 2. Navigate to the repository folder
# 3. Run this script
# Test with preprocessing and a formula
NXF_VER=20.04.1 nextflow run main.nf \
-c nextflow.config \
-profile testing \
--manifest data/mock.manifest.csv \
--nopreprocess \
--output output \
--hg_index data/hg_chr_21_bwa_index.tar.gz \
--formula "label1 + label2" \
--distance_threshold 0.5 \
-w work/ \
--noannot \
-resume \
-with-docker ubuntu:20.04
# # Test with preprocessing and a formula
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --manifest data/mock.manifest.csv \
# --preprocess_output output/preprocess_output \
# --output output1 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# --formula "label1 + label2" \
# --distance_threshold 0.1 \
# -w work/ \
# --noannot \
# --savereads \
# -resume
# # Test with preprocessing and no formula
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --manifest data/mock.manifest.csv \
# --preprocess_output output/preprocess_output \
# --output output2 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# --distance_threshold 0.1 \
# -w work/ \
# --noannot \
# -resume
# # Test with formula and no preprocessing
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --nopreprocess \
# --manifest data/mock.manifest.csv \
# --output output3 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# --formula "label1 + label2" \
# --distance_threshold 0.1 \
# -w work/ \
# --noannot \
# -resume
# # Test with no formula and no preprocessing
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --nopreprocess \
# --manifest data/mock.manifest.csv \
# --output output4 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# -w work/ \
# --noannot \
# -resume
# # Test with the gene catalog made in a previous round
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --gene_fasta output1/ref/genes.fasta.gz \
# --nopreprocess \
# --manifest data/mock.manifest.csv \
# --output output5 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# -w work/ \
# --noannot \
# -resume
# # Test with the gene catalog made in a previous round and whole genome alignment
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --gene_fasta output1/ref/genes.fasta.gz \
# --nopreprocess \
# --manifest data/mock.manifest.csv \
# --output output6 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# -w work/ \
# --eggnog_db false \
# --eggnog_dmnd false \
# --taxonomic_dmnd false \
# --ref_genome_fasta data/reference_genomes.fasta.gz \
# --ref_genome_csv data/reference_genomes.csv.gz \
# -resume
# # Test with de novo assembly and whole genome alignment
# NXF_VER=20.04.1 nextflow run main.nf \
# -c nextflow.config \
# -profile testing \
# --nopreprocess \
# --manifest data/mock.manifest.csv \
# --output output7 \
# --hg_index data/hg_chr_21_bwa_index.tar.gz \
# --distance_threshold 0.1 \
# -w work/ \
# --eggnog_db false \
# --eggnog_dmnd false \
# --taxonomic_dmnd false \
# --ref_genome_fasta data/reference_genomes.fasta.gz \
# --ref_genome_csv data/reference_genomes.csv.gz \
# -resume