Merge pull request #4 from LUMC/singularity

Singularity support 

.gitlab-ci.yml

@@ -30,6 +30,21 @@ test_dry_run:
     - docker
   stage: dry-run
 
+
+# this requires a priviliged docker container.
+# most docker runners will not do this
+test_integration_singularity:
+  before_script:
+    - apt-get update && apt-get install -y python3-pip
+    - pip3 install pyfaidx
+    - pip3 install -r requirements-dev.txt
+  script:
+    - py.test --tag singularity-integration
+  image: lumc/singularity-snakemake:3.0.3-5.4.0
+  tags:
+    - docker
+  stage: integration
+
 test_integration:
   before_script:
     - export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)

README.md

@@ -15,34 +15,75 @@ GATK HaplotypeCaller.
     * 96 exomes in < 24 hours.
 * No unnecessary jobs
 * Coverage metrics for any number of bed files.
-* Separate conda environments for **every** step. No more dependency hell!
-Every job can potentially use different versions of the same package.
+* Fully containerized rules through singularity and biocontainers. Legacy 
+conda environments are available as well.  
 * Optionally sub-sample inputs when number of bases exceeds a user-defined
 threshold.
 
 # Installation
 
-We recommend the use of [conda](https://conda.io/docs/) for installing all
-dependencies. All rules have a separate conda environment, which guarantees
-every tool can use its own dependencies.
+To run this pipeline you will need the following at minimum:
 
-To install the base environment containing snakemake itself, activate conda
-and run the following in your terminal:
+* python 3.6
+* snakemake 5.2.0 or newer
+* pyfaidx 
 
-`conda env create -f environment.yml`
+This repository contains a [conda](https://conda.io/docs/) 
+environment file that you can use to install all minimum dependencies in a 
+conda environment:
+
+```bash
+conda env create -f environment.yml
+``` 
+
+Alternatively, you can set up a python virtualenv and run
+
+```bash
+pip install -r requirements.txt
+```
+
+## Singularity 
+
+We highly recommend the user of the containerized rules through 
+[singularity](https://www.sylabs.io/singularity/).
+
+This option does, however,
+require you to install singularity on your system. As this usually requires 
+administrative privileges, singularity is not contained within our provided
+conda environment file.
+
+If you want to use singularity, make sure you install version 3 or higher. 
+
+### Debian
+If you happen to use Debian buster, singularity 3.0.3 comes straight out
+of the box with a simple:
+
+```bash
+sudo apt install singularity-container 
+```
+
+### Docker
+
+You can run singularity within a docker container. Please note that 
+the container **MUST** run in privileged mode for this to work. 
+
+We have provided our own container that includes singularity and snakemake
+[here](https://hub.docker.com/r/lumc/singularity-snakemake). 
+
+### Manual install
+
+If you don't use Debian buster and cannot run a privileged docker container,
+you - unfortunately :-( - will have to install singularity manually. 
+Please see the installation instructions 
+[here](https://github.com/sylabs/singularity/blob/master/INSTALL.md) on how
+to do that. 
 
-Subsequently running the pipeline with `--use-conda` will make sure 
-the correct conda environments get created. This requires a working
-internet connection. If you do not want conda environment to be created for
-each pipeline run, use the `--conda-prefix` argument. See the
-[snakemake documentation](http://snakemake.readthedocs.io/en/stable/executable.html)
-for more information. 
 
 ## GATK
 
-For license reasons, conda cannot fully install the GATK. The JAR 
+For license reasons, conda and singularity cannot fully install the GATK. The JAR 
 must be registered by running `gatk-register` after the environment is
-created, which conflicts with the automated environment creation.
+created, which conflicts with the automated environment/container creation.
  
 For this reason, hutspot **requires** you to manually specify the path to
 the GATK executable JAR via `--config GATK=/path/to/gatk.jar`.
@@ -86,7 +127,7 @@ the pipeline can be started with:
 
 ```bash
 snakemake -s Snakefile \
---use-conda \
+--use-singularity \
 --config <CONFIGURATION VALUES>
 ```
 
@@ -139,13 +180,34 @@ snakemake -s Snakefile \
 --drmaa ' -pe <PE_NAME> {cluster.threads} -q all.q -l h_vmem={cluster.vmem} -cwd -V -N hutspot' \
 ```
 
+## Binding additional directories under singularity
+
+In singularity mode, snakemake binds the location of itself in the container. 
+The current working directory is also visible directly in the container. 
+
+In many cases, this is not enough, and will result in `FileNotFoundError`s.
+E.g., suppose you run your pipeline in `/runs`, but your fastq files live in 
+`/fastq` and your reference genome lives in `/genomes`. We would have to bind
+`/fastq` and `/genomes` in the container. 
+
+This can be accomplished with `--singularity-args`, which accepts a simple 
+string of arguments passed to singularity. E.g. in the above example,
+we could do:
+
+```bash
+snakemake -S Snakefile \
+--use-singularity  \ 
+--singularity-args ' --bind /fastq:/fastq --bind /genomes:/genomes '
+```
+
 ## Summing up
 
 To sum up, a full pipeline run under a cluster would be called as:
 
 ```bash
 snakemake -s Snakefile \
---use-conda \
+--use-singularity \
+--singularity-args ' --bind /some_path:/some_path ' \
 --cluster-config cluster/sge-cluster.yml \
 --drmaa ' -pe <PE_NAME> {cluster.threads} -q all.q -l h_vmem={cluster.vmem} -cwd -V -N hutspot' \
 --rerun-incomplete \
@@ -163,6 +225,21 @@ FASTQ_COUNT=/path/to/fastq-count \
 BED=/path/to/interesting_region.bed
 ```
 
+## Using conda in stead of singularity
+
+Legacy conda environments are also available for each and every rule. 
+Simply use `--use-conda` in stead of `--use-singularity` to enable conda
+environments.
+
+As dependency conflicts can and do arise with conda, it is recommended to 
+combine this flag with `--conda-prefix`, such that you only have to 
+build the environments once.
+
+The conda environments use the same versions of tools as the singularity
+containers, bar one:
+
+* `fastqc` uses version 0.11.5 on conda, but 0.11.7 on singularity.    
+
 # Graph
 
 Below you can see the rulegraph of the pipeline. The main variant calling flow

Snakefile

@@ -193,24 +193,28 @@ rule all:
 rule create_markdup_tmp:
     """Create tmp directory for mark duplicates"""
     output: directory("tmp")
+    singularity: "docker://debian:buster-slim"
     shell: "mkdir -p {output}"
 
 rule genome:
     """Create genome file as used by bedtools"""
     input: REFERENCE
     output: "current.genome"
+    singularity: "docker://debian:buster-slim"
     shell: "awk -v OFS='\t' {{'print $1,$2'}} {input}.fai > {output}"
 
 rule merge_r1:
     """Merge all forward fastq files into one"""
     input: get_r1
     output: temp("{sample}/pre_process/{sample}.merged_R1.fastq.gz")
+    singularity: "docker://debian:buster-slim"
     shell: "cat {input} > {output}"
 
 rule merge_r2:
     """Merge all reverse fastq files into one"""
     input: get_r2
     output: temp("{sample}/pre_process/{sample}.merged_R2.fastq.gz")
+    singularity: "docker://debian:buster-slim"
     shell: "cat {input} > {output}"
 
 
@@ -225,6 +229,7 @@ rule seqtk_r1:
     output:
         fastq=temp("{sample}/pre_process/{sample}.sampled_R1.fastq.gz")
     conda: "envs/seqtk.yml"
+    singularity: "docker://quay.io/biocontainers/mulled-v2-13686261ac0aa5682c680670ff8cda7b09637943:d143450dec169186731bb4df6f045a3c9ee08eb6-0"
     shell: "bash {input.seqtk} {input.stats} {input.fastq} {output.fastq} "
            "{params.max_bases}"
 
@@ -240,6 +245,7 @@ rule seqtk_r2:
     output:
         fastq = temp("{sample}/pre_process/{sample}.sampled_R2.fastq.gz")
     conda: "envs/seqtk.yml"
+    singularity: "docker://quay.io/biocontainers/mulled-v2-13686261ac0aa5682c680670ff8cda7b09637943:d143450dec169186731bb4df6f045a3c9ee08eb6-0"
     shell: "bash {input.seqtk} {input.stats} {input.fastq} {output.fastq} "
            "{params.max_bases}"
 
@@ -256,6 +262,7 @@ rule sickle:
         r1 = temp("{sample}/pre_process/{sample}.trimmed_R1.fastq"),
         r2 = temp("{sample}/pre_process/{sample}.trimmed_R2.fastq"),
         s = "{sample}/pre_process/{sample}.trimmed_singles.fastq"
+    singularity: "docker://quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4"
     conda: "envs/sickle.yml"
     shell: "sickle pe -f {input.r1} -r {input.r2} -t sanger -o {output.r1} "
            "-p {output.r2} -s {output.s}"
@@ -268,6 +275,7 @@ rule cutadapt:
     output:
         r1 = temp("{sample}/pre_process/{sample}.cutadapt_R1.fastq"),
         r2 = temp("{sample}/pre_process/{sample}.cutadapt_R2.fastq")
+    singularity: "docker://quay.io/biocontainers/cutadapt:1.14--py36_0"
     conda: "envs/cutadapt.yml"
     shell: "cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -m 1 -o {output.r1} "
            "{input.r1} -p {output.r2} {input.r2}"
@@ -281,6 +289,7 @@ rule align:
     params:
         rg = "@RG\\tID:{sample}_lib1\\tSM:{sample}\\tPL:ILLUMINA"
     output: temp("{sample}/bams/{sample}.sorted.bam")
+    singularity: "docker://quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0"
     conda: "envs/bwa.yml"
     shell: "bwa mem -t 8 -R '{params.rg}' {input.ref} {input.r1} {input.r2} "
            "| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null "
@@ -295,6 +304,7 @@ rule markdup:
         bam = "{sample}/bams/{sample}.markdup.bam",
         bai = "{sample}/bams/{sample}.markdup.bai",
         metrics = "{sample}/bams/{sample}.markdup.metrics"
+    singularity: "docker://quay.io/biocontainers/picard:2.14--py36_0"
     conda: "envs/picard.yml"
     shell: "picard -Xmx4G MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
            "INPUT={input.bam} OUTPUT={output.bam} "
@@ -307,6 +317,7 @@ rule bai:
         bai = "{sample}/bams/{sample}.markdup.bai"
     output:
         bai = "{sample}/bams/{sample}.markdup.bam.bai"
+    singularity: "docker://debian:buster-slim"
     shell: "cp {input.bai} {output.bai}"
 
 rule baserecal:
@@ -320,6 +331,7 @@ rule baserecal:
         hapmap = HAPMAP
     output:
         grp = "{sample}/bams/{sample}.baserecal.grp"
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     conda: "envs/gatk.yml"
     shell: "java -XX:ParallelGCThreads=1 -jar {input.gatk} -T "
            "BaseRecalibrator -I {input.bam} -o {output.grp} -nct 8 "
@@ -341,6 +353,7 @@ rule gvcf_scatter:
     output:
         gvcf=temp("{sample}/vcf/{sample}.{chunk}.part.vcf.gz"),
         gvcf_tbi=temp("{sample}/vcf/{sample}.{chunk}.part.vcf.gz.tbi")
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     conda: "envs/gatk.yml"
     shell: "java -jar -Xmx4G -XX:ParallelGCThreads=1 {input.gatk} "
            "-T HaplotypeCaller -ERC GVCF -I "
@@ -364,6 +377,7 @@ rule gvcf_gather:
                                    chunk=CHUNKS))
     output:
         gvcf="{sample}/vcf/{sample}.g.vcf.gz"
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     conda: "envs/gatk.yml"
     shell: "java -Xmx4G -XX:ParallelGCThreads=1 -cp {input.gatk} "
            "org.broadinstitute.gatk.tools.CatVariants "
@@ -384,6 +398,7 @@ rule genotype_scatter:
     output:
         vcf=temp("multisample/genotype.{chunk}.part.vcf.gz"),
         vcf_tbi=temp("multisample/genotype.{chunk}.part.vcf.gz.tbi")
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     conda: "envs/gatk.yml"
     shell: "java -jar -Xmx15G -XX:ParallelGCThreads=1 {input.gatk} -T "
            "GenotypeGVCFs -R {input.ref} "
@@ -404,6 +419,7 @@ rule genotype_gather:
     output:
         combined="multisample/genotyped.vcf.gz"
     conda: "envs/gatk.yml"
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     shell: "java -Xmx4G -XX:ParallelGCThreads=1 -cp {input.gatk} "
            "org.broadinstitute.gatk.tools.CatVariants "
            "-R {input.ref} -V '{params.vcfs}' -out {output.combined} "
@@ -420,6 +436,7 @@ rule split_vcf:
         s="{sample}"
     output:
         splitted="{sample}/vcf/{sample}_single.vcf.gz"
+    singularity: "docker://quay.io/biocontainers/gatk:3.7--py36_1"
     conda: "envs/gatk.yml"
     shell: "java -Xmx15G -XX:ParallelGCThreads=1 -jar {input.gatk} "
            "-T SelectVariants -sn {params.s} -env -R {input.ref} -V "
@@ -434,6 +451,7 @@ rule mapped_num:
         bam="{sample}/bams/{sample}.sorted.bam"
     output:
         num="{sample}/bams/{sample}.mapped.num"
+    singularity: "docker://quay.io/biocontainers/samtools:1.6--he673b24_3"
     conda: "envs/samtools.yml"
     shell: "samtools view -F 4 {input.bam} | wc -l > {output.num}"
 
@@ -444,6 +462,7 @@ rule mapped_basenum:
         bam="{sample}/bams/{sample}.sorted.bam"
     output:
         num="{sample}/bams/{sample}.mapped.basenum"
+    singularity: "docker://quay.io/biocontainers/samtools:1.6--he673b24_3"
     conda: "envs/samtools.yml"
     shell: "samtools view -F 4 {input.bam} | cut -f10 | wc -c > {output.num}"
 
@@ -454,6 +473,7 @@ rule unique_num:
         bam="{sample}/bams/{sample}.markdup.bam"
     output:
         num="{sample}/bams/{sample}.unique.num"
+    singularity: "docker://quay.io/biocontainers/samtools:1.6--he673b24_3"
     conda: "envs/samtools.yml"
     shell: "samtools view -F 4 -F 1024 {input.bam} | wc -l > {output.num}"
 
@@ -464,6 +484,7 @@ rule usable_basenum:
         bam="{sample}/bams/{sample}.markdup.bam"
     output:
         num="{sample}/bams/{sample}.usable.basenum"
+    singularity: "docker://quay.io/biocontainers/samtools:1.6--he673b24_3"
     conda: "envs/samtools.yml"
     shell: "samtools view -F 4 -F 1024 {input.bam} | cut -f10 | wc -c > "
            "{output.num}"
@@ -472,7 +493,11 @@ rule usable_basenum:
 ## fastqc
 
 rule fastqc_raw:
-    """Run fastqc on raw fastq files"""
+    """
+    Run fastqc on raw fastq files
+    NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to 
+    perl missing in the container of 0.11.5
+    """
     input:
         r1=get_r1,
         r2=get_r2
@@ -480,13 +505,18 @@ rule fastqc_raw:
         odir="{sample}/pre_process/raw_fastqc"
     output:
         aux="{sample}/pre_process/raw_fastqc/.done.txt"
+    singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
     conda: "envs/fastqc.yml"
     shell: "fastqc --nogroup -o {params.odir} {input.r1} {input.r2} "
            "&& echo 'done' > {output.aux}"
 
 
 rule fastqc_merged:
-    """Run fastqc on merged fastq files"""
+    """
+    Run fastqc on merged fastq files    
+    NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to 
+    perl missing in the container of 0.11.5
+    """
     input:
         r1="{sample}/pre_process/{sample}.merged_R1.fastq.gz",
         r2="{sample}/pre_process/{sample}.merged_R2.fastq.gz",
@@ -496,13 +526,18 @@ rule fastqc_merged:
     output:
         r1="{sample}/pre_process/merged_fastqc/{sample}.merged_R1_fastqc.zip",
         r2="{sample}/pre_process/merged_fastqc/{sample}.merged_R2_fastqc.zip"
+    singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
     conda: "envs/fastqc.yml"
     shell: "bash {input.fq} {input.r1} {input.r2} "
            "{output.r1} {output.r2} {params.odir}"
 
 
 rule fastqc_postqc:
-    """Run fastqc on fastq files post pre-processing"""
+    """
+    Run fastqc on fastq files post pre-processing
+    NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to 
+    perl missing in the container of 0.11.5     
+    """
     input:
         r1="{sample}/pre_process/{sample}.cutadapt_R1.fastq",
         r2="{sample}/pre_process/{sample}.cutadapt_R2.fastq",
@@ -512,6 +547,7 @@ rule fastqc_postqc:
     output:
         r1="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
         r2="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R2_fastqc.zip"
+    singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
     conda: "envs/fastqc.yml"
     shell: "bash {input.fq} {input.r1} {input.r2} "
            "{output.r1} {output.r2} {params.odir}"
@@ -526,6 +562,7 @@ rule fqcount_preqc:
         r2="{sample}/pre_process/{sample}.merged_R2.fastq.gz"
     output:
         "{sample}/pre_process/{sample}.preqc_count.json"
+    singularity: "docker://quay.io/biocontainers/fastq-count:0.1.0--h14c3975_0"
     conda: "envs/fastq-count.yml"
     shell: "fastq-count {input.r1} {input.r2} > {output}"
 
@@ -537,6 +574,7 @@ rule fqcount_postqc:
         r2="{sample}/pre_process/{sample}.cutadapt_R2.fastq"
     output:
         "{sample}/pre_process/{sample}.postqc_count.json"
+    singularity: "docker://quay.io/biocontainers/fastq-count:0.1.0--h14c3975_0"
     conda: "envs/fastq-count.yml"
     shell: "fastq-count {input.r1} {input.r2} > {output}"
 
@@ -550,6 +588,7 @@ rule fastqc_stats:
         postqc_r1="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
         postqc_r2="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R2_fastqc.zip",
         sc=fqpy
+    singularity: "docker://python:3.6-slim"
     conda: "envs/collectstats.yml"
     output:
         "{sample}/pre_process/fastq_stats.json"
@@ -572,6 +611,7 @@ rule covstats:
     output:
         covj="{sample}/coverage/{bed}.covstats.json",
         covp="{sample}/coverage/{bed}.covstats.png"
+    singularity: "docker://quay.io/biocontainers/mulled-v2-3251e6c49d800268f0bc575f28045ab4e69475a6:4ce073b219b6dabb79d154762a9b67728c357edb-0"
     conda: "envs/covstat.yml"
     shell: "bedtools coverage -sorted -g {input.genome} -a {input.bed} "
            "-b {input.bam} -d  | python {input.covpy} - --plot {output.covp} "
@@ -586,6 +626,7 @@ rule vtools_coverage:
         ref=get_refflatpath
     output:
         tsv="{sample}/coverage/{ref}.coverages.tsv"
+    singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
     conda: "envs/vcfstats.yml"
     shell: "vtools-gcoverage -I {input.gvcf} -R {input.ref} > {output.tsv}"
 
@@ -598,6 +639,7 @@ rule vcfstats:
         vcf="multisample/genotyped.vcf.gz"
     output:
         stats="multisample/vcfstats.json"
+    singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
     conda: "envs/vcfstats.yml"
     shell: "vtools-stats -i {input.vcf} > {output.stats}"
 
@@ -622,6 +664,7 @@ if len(BASE_BEDS) >= 1:
             fthresh=FEMALE_THRESHOLD
         output:
             "{sample}/{sample}.stats.json"
+        singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
         conda: "envs/collectstats.yml"
         shell: "python {input.colpy} --sample-name {params.sample_name} "
                "--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} "
@@ -646,6 +689,7 @@ else:
             fthresh = FEMALE_THRESHOLD
         output:
             "{sample}/{sample}.stats.json"
+        singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
         conda: "envs/collectstats.yml"
         shell: "python {input.colpy} --sample-name {params.sample_name} "
                "--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} "
@@ -662,6 +706,7 @@ rule merge_stats:
         mpy=mpy
     output:
         stats="stats.json"
+    singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
     conda: "envs/collectstats.yml"
     shell: "python {input.mpy} --vcfstats {input.vstat} {input.cols} "
            "> {output.stats}"
@@ -674,6 +719,7 @@ rule stats_tsv:
         sc=tsvpy
     output:
         stats="stats.tsv"
+    singularity: "docker://python:3.6-slim"
     conda: "envs/collectstats.yml"
     shell: "python {input.sc} -i {input.stats} > {output.stats}"
 
@@ -690,5 +736,6 @@ rule multiqc:
         rdir="multiqc_report"
     output:
         report="multiqc_report/multiqc_report.html"
+    singularity: "docker://quay.io/biocontainers/multiqc:1.5--py36_0"
     conda: "envs/multiqc.yml"
     shell: "multiqc -f -o {params.rdir} {params.odir} || touch {output.report}"

envs/seqtk.yml

@@ -5,6 +5,12 @@ channels:
   - defaults
 dependencies:
   - bc=1.06
+  - flex=2.6.4
+  - jq=1.6
+  - libgcc-ng=8.2.0
+  - libstdcxx-ng=8.2.0
+  - m4=1.4.18
+  - oniguruma=6.9.2
   - sed=4.4
   - seqtk=1.2
   - zlib=1.2.11
\ No newline at end of file

envs/vcfstats.yml

@@ -40,4 +40,4 @@ dependencies:
   - vtools=1.0.0
   - wheel=0.33.4
   - xz=5.2.4
-  - zlib=1.2.11
\ No newline at end of file
+  - zlib=1.2.11

src/safe_fastqc.sh

@@ -26,13 +26,13 @@ odir=${5}
 fastqc --nogroup -o ${odir} ${input_r1} ${input_r2}
 
 if [[ -f ${output_r1} ]]; then
-    unzip -t ${output_r1} || truncate -s0 ${output_r1}
+    unzip -l ${output_r1} || head -c 0 ${output_r1} > ${output_r1}
 else
     touch ${output_r1}
 fi
 
 if [[ -f ${output_r2} ]]; then
-    unzip -t ${output_r2} || truncate -s0 ${output_r2}
+    unzip -l ${output_r2} || head -c 0 ${output_r2} > ${output_r2}
 else
     touch ${output_r2}
 fi

tests/test_integration_run.yml

@@ -3,8 +3,7 @@
     bash -c '
     snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
     --cluster "sbatch --parsable" -r -p -s Snakefile
-    --config JAVA=$(which java)
-    REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
+    --config REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
     DBSNP=tests/data/database.vcf.gz
     ONETHOUSAND=tests/data/database.vcf.gz
     HAPMAP=tests/data/database.vcf.gz
@@ -19,3 +18,23 @@
       - "rror"
   tags:
     - integration
+- name: test-singularity-integration-no-cluster
+  command: >-
+    bash -c '
+    snakemake --use-singularity --jobs 100 -w 120
+    -r -p -s Snakefile
+    --config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa
+    DBSNP=tests/data/database.vcf.gz
+    ONETHOUSAND=tests/data/database.vcf.gz
+    HAPMAP=tests/data/database.vcf.gz
+    SAMPLE_CONFIG=tests/data/sample_config.json'
+  exit_code: 0
+  stderr:
+    contains:
+      - "Job counts"
+      - "localrule all:"
+      - "(100%) done"
+    must_not_contain:
+      - "rror"
+  tags:
+    - singularity-integration
\ No newline at end of file