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R2915/singularity-pipeline-runner/bioinformatics_pipeline2.yaml
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bioinformatics_pipeline2.yaml
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name: bioinformatics pipeline 2
version: 1
author:
author_org:
source:
build:
type: bootstrap
source: bioinformatics_pipeline2.singularity
size: 2048
substitutions:
RefGenome: "./scicore-pipeline2-input-data/RefGenome/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/"
run:
commands:
- "[ -d output/bowtie2 ] || mkdir -p output/bowtie2"
- "[ -d output/samtools ] || mkdir -p output/samtools"
- "[ -d output/freebayes ] || mkdir -p output/freebayes"
- "echo 'aligning reads with bowtie2...'"
- "singularity exec {image} bowtie2 -p ${{NUM_CPUS}} -x {RefGenome}/Bowtie2Index/genome -q -1 scicore-pipeline2-input-data/fastq/SRR5511076_1.ds.fastq -2 scicore-pipeline2-input-data/fastq/SRR5511076_2.ds.fastq -S output/bowtie2/yeast_reseq_ds-bt2aln.sam"
- "echo 'SAM to sorted BAM...'"
- "singularity exec {image} samtools view -bS output/bowtie2/yeast_reseq_ds-bt2aln.sam | singularity exec {image} samtools sort - --threads ${{NUM_CPUS}} -o output/samtools/yeast_reseq_ds-bt2aln.s.bam"
- "echo 'calling variants with FreeBayes...'"
- "singularity exec {image} freebayes -f {RefGenome}/WholeGenomeFasta/genome.fa output/samtools/yeast_reseq_ds-bt2aln.s.bam > output/freebayes/yeast_reseq_ds-bt2aln.s.vcf"
test:
test_files:
- scicore-pipeline2-input-data.tar.gz
- scicore-pipeline2-input-data
- output.md5
prepare_commands:
- "echo '33921b7c4b3d3f3da638d9aa517c0a07 -' > output.md5"
- "wget -O scicore-pipeline2-input-data.tar.gz http://users.scicore.unibas.ch/~escobar/data/scicore-pipeline2-input-data.tar.bz2"
- "tar xzf scicore-pipeline2-input-data.tar.gz"
validate_commands:
- "singularity exec {image} vcftools --vcf output/freebayes/yeast_reseq_ds-bt2aln.s.vcf --FILTER-summary --stdout | md5sum -c output.md5"
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