changed directory structure: tests go2 test/

.gitignore

@@ -25,4 +25,11 @@ nohup.out
 
 .snakemake/
 no_backup/
-test/*/
+test/results/*/
+
+coverage_check/
+test/benchmarks/
+test/params_files/
+test/run-tests.sh
+tmp/
+

envs/nextflow.yml.bak

-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

params_files/nanopore_multi.yaml

-nanopore:
- - data_prep/nanopore.sim.100.fastq
- - data_prep/nanopore.sim.101.fastq
- - data_prep/nanopore.sim.102.fastq

params_files/pacbio_multi.yaml

-pacbio:
- - data_prep/pacbio.10000.1.fastq
- - data_prep/pacbio.10000.5.fastq
- - data_prep/pacbio.10000.9.fastq

params_files/paired_multi.yaml

-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

params_files/single_multi.yaml

-single-end:
- - data_prep/unpaired.100.1.fastq
- - data_prep/unpaired.100.5.fastq
- - data_prep/unpaired.100.9.fastq

Snakefile → test/Snakefile

@@ -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:

config.yml → test/config.yml

 ---
 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