github.com/informationsea/shellflow@v0.1.3/README.md (about)

     1  Shellflow
     2  =========
     3  
     4  [![Build Status](https://travis-ci.org/informationsea/shellflow.svg?branch=master)](https://travis-ci.org/informationsea/shellflow)
     5  [![Documentation Status](https://readthedocs.org/projects/shellflow/badge/?version=latest)](https://shellflow.readthedocs.io/en/latest/?badge=latest)
     6  
     7  Shell Script like scientific workflow management system
     8  
     9  # Licnese
    10  
    11  GPL version 3 or later
    12  
    13  # Documents
    14  
    15  Available at [Read the docs](https://shellflow.readthedocs.io/en/latest/)
    16  
    17  # Example
    18  
    19  ```bash
    20  #% GATK_VERSION = "4.0.10.1"
    21  #% BWA_VERSION = "0.7.17"
    22  #% SAMTOOLS_VERSION = "1.9"
    23  
    24  # Generate simulation FASTQ
    25  python3 ((create-mutated-fasta.py)) ((e-coli-NC_011750.1.fasta)) --output [[e-coli-NC_011750.1-mutated-base.fasta]] --seed 123
    26  for i in 1 2; do
    27      python3 ((create-mutated-fasta.py)) ((e-coli-NC_011750.1-mutated-base.fasta)) --output [[e-coli-NC_011750.1-mutated{{i}}.fasta]] --seed 123{{i}}
    28      art_bin_MountRainier/art_illumina -ss HS25 -i ((e-coli-NC_011750.1-mutated{{i}}.fasta)) -p -l 150 -f 20 -m 200 -s 10 -o generated{{i}} # [[generated{{i}}1.fq]] [[generated{{i}}2.fq]]
    29      for j in 1 2; do
    30          sed -e 's/@/@{{i}}-/g' ((generated{{i}}{{j}}.fq))|gzip -c > [[generated{{i}}{{j}}-fix.fq.gz]]
    31      done
    32  done
    33  
    34  # Mapping
    35  for i in 1 2; do
    36      bwa-{{BWA_VERSION}}/bwa mem -R "@RG\tID:ECOLI-SIM\tSM:ECOLI_SIM\tPL:illumina\tLB:ECOLI_SIM" e-coli-NC_011750.1.fasta ((generated{{i}}1-fix.fq.gz)) ((generated{{i}}2-fix.fq.gz))|samtools-{{SAMTOOLS_VERSION}}/samtools sort -o [[generated{{i}}.bam]] - # ((e-coli-NC_011750.1.fasta.bwt))
    37      gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4G" MarkDuplicates -I ((generated{{i}}.bam)) -O [[generated{{i}}-markdup.bam]] -M [[generated{{i}}-markdup-metrics.txt]]
    38      gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4G" BaseRecalibrator -I ((generated{{i}}-markdup.bam)) -O [[generated{{i}}-bqsr.txt]] -R ((e-coli-NC_011750.1.fasta)) --known-sites ((empty.vcf.gz)) # ((e-coli-NC_011750.1.dict))
    39  done
    40  
    41  gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4G" GatherBQSRReports -I ((generated1-bqsr.txt)) -I ((generated2-bqsr.txt)) -O [[generated-bqsr-merged.txt]]
    42  
    43  # Apply BQSR
    44  for i in 1 2; do
    45      gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4G" ApplyBQSR -R ((e-coli-NC_011750.1.fasta)) -I ((generated{{i}}-markdup.bam)) -O [[generated{{i}}-recal.bam]] --bqsr-recal-file ((generated-bqsr-merged.txt)) # ((e-coli-NC_011750.1.dict))
    46  done
    47  
    48  # Merge
    49  
    50  samtools-{{SAMTOOLS_VERSION}}/samtools merge -f [[generated-merged.bam]] ((generated1-recal.bam)) ((generated2-recal.bam))
    51  samtools-{{SAMTOOLS_VERSION}}/samtools index ((generated-merged.bam)) # [[generated-merged.bam.bai]]
    52  
    53  # Variant call
    54  gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4g" HaplotypeCaller -R ((e-coli-NC_011750.1.fasta)) -I ((generated-merged.bam)) -O [[generated-call.vcf.gz]] -ERC GVCF -bamout [[generated-merged-realigned.bam]] # ((e-coli-NC_011750.1.dict)) ((generated-merged.bam.bai))
    55  gatk-{{GATK_VERSION}}/gatk --java-options "-Xmx4g" GenotypeGVCFs -R ((e-coli-NC_011750.1.fasta)) -V ((generated-call.vcf.gz)) -O [[generated-call-result.vcf.gz]] # ((e-coli-NC_011750.1.dict))
    56  ```