Commit 5409bd9e authored by Sander Bollen's avatar Sander Bollen
Browse files

fix too many spaces

parent 1d7a6bd9
Pipeline #2553 passed with stages
in 21 minutes and 7 seconds
......@@ -263,7 +263,7 @@ 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 "
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}"
......@@ -276,7 +276,7 @@ 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 "
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}"
......@@ -715,6 +715,6 @@ rule multiqc:
rdir="multiqc_report"
output:
report="multiqc_report/multiqc_report.html"
singularity: "docker://quay.io/biocontainers/multiqc:1.5--py36_0 "
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}"
......@@ -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
......
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