A compact version of Oxford Compass (Complete Pathogen Analytical Software Solution)
A nextflow-docker paired pipeline for processing pathogen bacterial sequencing data generated using Illumina sequencing platform. It runs following:
1. Take paired fastq files or bam files in a file folder
2. Map reads to reference genome using Stampy (main_stampy.nf) or BWA (main_bwa.nf)
3. SNP calling using samtools and bcftools, and
4. Annotate VCF using masked reference and create a consensus sequence fasta file
input files directory
fastq or bam files pattern
reference genome
*.basecallstats.txt
*.consensus.fasta.gz
*.basecall_indel.vcf.gz
*.basecall.vcf.gz
docker pull oxfordmmm/compasscompact:{version} nextflow run main_stampy.nf --help
nextflow run main_stampy.nf --test -profile test_docker
nextflow run main_stampy.nf \
--input_dir tests/data/input_dir/ \
--output_dir tests/data/output_dir \
--ref tests/data/reference/NC_000962_2.fasta \
--fastq true \
--pattern "*_{1,2}.fastq.gz" \
-profile test_docker
nextflow run main_stampy.nf \
--input_dir tests/data/input_dir/ \
--output_dir tests/data/output_dir \
--ref tests/data/reference/NC_000962_2.fasta \
--fastq false \
--pattern "*.bam" \
-profile test_docker --input_dir DIR path of fastq files, or bam files
--fastq Boolean Input files are fastq format
--pattern String fastq file name pattern, such as "*_{1,2}.fastq.gz"
--output_dir DIR path for transformed fastq files
--ref FILE reference genome --threads INT number of threads to run, default 41. Copy a pair input fastq files or a bam file to tests/data/test_input
2. Copy genomo reference fasta as tests/data/reference/NC_000962_3.fasta
3. Copy expected basecall output fasta to tests/data/test_output/expected_output
python3 tests/test_stampy.py bam (under CompassCompact, test bam input)
python3 tests/test_stampy.py fastq (under CompassCompact, test fastq input)The test will run the stampy nextflow pipeline and compare the output fasta file with expected fasta file.
docker pull oxfordmmm/compasscompact:{version} nextflow run mask_ref.nf --help
nextflow run mask_ref.nf --test -profile test_docker
nextflow run mask_ref.nf \
--output_dir tests/data/output_dir \
--ref tests/data/reference/NC_000962_2.fasta \
--mask true \
-profile test_docker --ref FILE reference genome --mask Boolean use self-blast to mask repeated region, default true nextflow run main_bwa.nf --help
nextflow run main_bwa.nf --test
nextflow run main_bwa.nf \
--input_dir tests/data/input_dir/ \
--output_dir tests/data/output_dir \
--ref tests/data/reference/NC_000962_3.fasta \
--mask_file "tests/data/reference/NC_000962_3_repmask.array" \
--fastq true \
--pattern "*_{1,2}.fastq.gz" \
-profile test_docker
nextflow run main_bwa.nf --input_dir tests/data/input_dir/ \
--output_dir tests/data/output_dir \
--ref tests/data/reference/NC_000962_3.fasta \
--mask_file = "tests/data/reference/NC_000962_3_repmask.array" \
--fastq false \
--pattern "*.bam" \
-profile test_docker
--input_dir DIR path of fastq files, or bam files
--fastq Boolean Input files are fastq format
--pattern String fastq file name pattern, such as "*_{1,2}.fastq.gz"
--output_dir DIR path for transformed fastq files
--ref FILE reference genome
--mask_file FILE reference mask array --threads INT number of threads to run, default 41. Copy a pair input fastq files or a bam file to tests/data/test_input
2. Copy genomo reference fasta as tests/data/reference/NC_000962_3.fasta
3. Copy genomo reference mask array as tests/data/reference/NC_000962_3_repmask.array
4. Copy expected basecall output fasta to tests/data/test_output/expected_output
python3 tests/test_bwa.py bam (under CompassCompact, test bam input)
python3 tests/test_bwa.py fastq (under CompassCompact, test fastq input)The test will run the bwa nextflow pipeline and compare the output fasta file with expected fasta file.
bwa-0.7.15
https://github.com/lh3/bwa
GenomeAnalysisTK-3.7-0
https://github.com/broadinstitute/gatk/
ncbi-blast-2.2.23+
https://blast.ncbi.nlm.nih.gov/Blast.cgi
picard-tools-1.123
https://github.com/broadinstitute/picard/
stampy-1.0.23
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106326/
samtools-1.4.1
https://github.com/samtools/samtools/releases
vcftools_0.1.9
https://vcftools.github.io/downloads.html
All bioinformatic tools are configured in `docker/compass/lib/compass.cfg`
To debug with different version of tools or parameters, change `nextflow.config` the volume host path
from `/home/docker/Code/CompassCompact/docker/compass`
to wherever the compass code directory is (typically, where you clone the reponsitory to + `/docker/compass`).