Commit 82ff70c4 authored by Raphael Müller's avatar Raphael Müller
Browse files

changed directory structure: tests go2 test/

parent b87fd4ea
......@@ -25,4 +25,11 @@ nohup.out
.snakemake/
no_backup/
test/*/
test/results/*/
coverage_check/
test/benchmarks/
test/params_files/
test/run-tests.sh
tmp/
name: backmap
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- snakemake
- mamba
- nextflow
- perl
- perl-app-cpanminus
- samtools
- bedtools
- bwa
- minimap2
- qualimap
- multiqc
- r-base
- r-ggplot2
- r-dplyr
nanopore:
- data_prep/nanopore.sim.100.fastq
- data_prep/nanopore.sim.101.fastq
- data_prep/nanopore.sim.102.fastq
pacbio:
- data_prep/pacbio.10000.1.fastq
- data_prep/pacbio.10000.5.fastq
- data_prep/pacbio.10000.9.fastq
paired-end:
- data_prep/paired_1.1000.1.fastq,data_prep/paired_2.1000.1.fastq
- data_prep/paired_1.1000.5.fastq,data_prep/paired_2.1000.5.fastq
- data_prep/paired_1.1000.9.fastq,data_prep/paired_2.1000.9.fastq
single-end:
- data_prep/unpaired.100.1.fastq
- data_prep/unpaired.100.5.fastq
- data_prep/unpaired.100.9.fastq
......@@ -77,6 +77,7 @@ rule all:
rules.assembly_single_paired_nextflow.output,
rules.bams_illumina_paired_pacbio_nanopore_perl.output,
rules.bams_illumina_paired_pacbio_nanopore_nextflow.output,
rules.bams_with_assembly_illumina_paired_pacbio_nanopore_nextflow.output,
rule data_prep:
......
---
benchmark_repeats: 3
workdir: "test"
datadir: "dataset1/"
original_perl_script: "perl original_wf/backmap/backmap.pl"
nextflow_script: "nextflow nextflow/backmap.nf -c nextflow/nextflow.config --threads 16"
assembly: "dataset1/dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta"
workdir: "results"
original_perl_script: "perl ../original_wf/backmap/backmap.pl"
nextflow_script: "nextflow ../nextflow/backmap.nf -c nextflow/nextflow.config --threads 16"
assembly: "../dataset1/dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta"
datadir: "../dataset1/"
unpaired: dgal.confilter.fq
paired_1: dgal_1.paired.confilter.fq
paired_2: dgal_2.paired.confilter.fq
......
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