github.com/informationsea/shellflow@v0.1.3/examples/doc-example3/analysis.dot (about)

     1  digraph shelltask {
     2    node [shape=box];
     3    task1 [label="bwa-0.7.17/bwa index e-coli-NC_011750.1.fasta # e-coli-NC_011750.1.fasta.bwt"];
     4    task2 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" CreateSequenceDictionary -R e-coli-NC_011750.1.fasta # e-coli-NC_011750.1.dict"];
     5    task3 [label="python3 create-mutated-fasta.py e-coli-NC_011750.1.fasta --output e-coli-NC_011750.1-mutated-base.fasta --seed 123"];
     6    task4 [label="python3 create-mutated-fasta.py e-coli-NC_011750.1-mutated-base.fasta --output e-coli-NC_011750.1-mutated1.fasta --seed 1231"];
     7    task5 [label="art_bin_MountRainier/art_illumina -ss HS25 -i e-coli-NC_011750.1-mutated1.fasta -p -l 150 -f 20 -m 200 -s 10 -o generated1 # generated11.fq generated12.fq"];
     8    task6 [label="sed -e 's/@/@1-/g' generated11.fq|gzip -c > generated11-fix.fq.gz"];
     9    task7 [label="sed -e 's/@/@1-/g' generated12.fq|gzip -c > generated12-fix.fq.gz"];
    10    task8 [label="python3 create-mutated-fasta.py e-coli-NC_011750.1-mutated-base.fasta --output e-coli-NC_011750.1-mutated2.fasta --seed 1232"];
    11    task9 [label="art_bin_MountRainier/art_illumina -ss HS25 -i e-coli-NC_011750.1-mutated2.fasta -p -l 150 -f 20 -m 200 -s 10 -o generated2 # generated21.fq generated22.fq"];
    12    task10 [label="sed -e 's/@/@2-/g' generated21.fq|gzip -c > generated21-fix.fq.gz"];
    13    task11 [label="sed -e 's/@/@2-/g' generated22.fq|gzip -c > generated22-fix.fq.gz"];
    14    task12 [label="bwa-0.7.17/bwa mem -R \"@RG\\tID:ECOLI-SIM\\tSM:ECOLI_SIM\\tPL:illumina\\tLB:ECOLI_SIM\" e-coli-NC_011750.1.fasta generated11-fix.fq.gz generated12-fix.fq.gz|samtools-1.9/samtools sort -o generated1.bam - # e-coli-NC_011750.1.fasta.bwt"];
    15    task13 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" MarkDuplicates -I generated1.bam -O generated1-markdup.bam -M generated1-markdup-metrics.txt"];
    16    task14 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" BaseRecalibrator -I generated1-markdup.bam -O generated1-bqsr.txt -R e-coli-NC_011750.1.fasta --known-sites empty.vcf.gz # e-coli-NC_011750.1.dict"];
    17    task15 [label="bwa-0.7.17/bwa mem -R \"@RG\\tID:ECOLI-SIM\\tSM:ECOLI_SIM\\tPL:illumina\\tLB:ECOLI_SIM\" e-coli-NC_011750.1.fasta generated21-fix.fq.gz generated22-fix.fq.gz|samtools-1.9/samtools sort -o generated2.bam - # e-coli-NC_011750.1.fasta.bwt"];
    18    task16 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" MarkDuplicates -I generated2.bam -O generated2-markdup.bam -M generated2-markdup-metrics.txt"];
    19    task17 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" BaseRecalibrator -I generated2-markdup.bam -O generated2-bqsr.txt -R e-coli-NC_011750.1.fasta --known-sites empty.vcf.gz # e-coli-NC_011750.1.dict"];
    20    task18 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" GatherBQSRReports -I generated1-bqsr.txt -I generated2-bqsr.txt -O generated-bqsr-merged.txt"];
    21    task19 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" ApplyBQSR -R e-coli-NC_011750.1.fasta -I generated1-markdup.bam -O generated1-recal.bam --bqsr-recal-file generated-bqsr-merged.txt # e-coli-NC_011750.1.dict"];
    22    task20 [label="gatk-4.0.10.1/gatk --java-options \"-Xmx4G\" ApplyBQSR -R e-coli-NC_011750.1.fasta -I generated2-markdup.bam -O generated2-recal.bam --bqsr-recal-file generated-bqsr-merged.txt # e-coli-NC_011750.1.dict"];
    23    task21 [label="samtools-1.9/samtools merge -f generated-merged.bam generated1-recal.bam generated2-recal.bam"];
    24    task22 [label="samtools-1.9/samtools index generated-merged.bam # generated-merged.bam.bai"];
    25    task23 [label="gatk-4.0.10.1/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"];
    26    task24 [label="gatk-4.0.10.1/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"];
    27    input0 [label="create-mutated-fasta.py", color=red];
    28    input0 -> task3;
    29    input0 -> task4;
    30    input0 -> task8;
    31    input1 [label="e-coli-NC_011750.1.fasta", color=red];
    32    input1 -> task1;
    33    input1 -> task2;
    34    input1 -> task3;
    35    input1 -> task14;
    36    input1 -> task17;
    37    input1 -> task19;
    38    input1 -> task20;
    39    input1 -> task23;
    40    input1 -> task24;
    41    input2 [label="empty.vcf.gz", color=red];
    42    input2 -> task14;
    43    input2 -> task17;
    44    task3 -> task4 [label="e-coli-NC_011750.1-mutated-base.fasta"];
    45    task4 -> task5 [label="e-coli-NC_011750.1-mutated1.fasta"];
    46    task5 -> task6 [label="generated11.fq"];
    47    task5 -> task7 [label="generated12.fq"];
    48    task3 -> task8 [label="e-coli-NC_011750.1-mutated-base.fasta"];
    49    task8 -> task9 [label="e-coli-NC_011750.1-mutated2.fasta"];
    50    task9 -> task10 [label="generated21.fq"];
    51    task9 -> task11 [label="generated22.fq"];
    52    task1 -> task12 [label="e-coli-NC_011750.1.fasta.bwt"];
    53    task6 -> task12 [label="generated11-fix.fq.gz"];
    54    task7 -> task12 [label="generated12-fix.fq.gz"];
    55    task12 -> task13 [label="generated1.bam"];
    56    task2 -> task14 [label="e-coli-NC_011750.1.dict"];
    57    task13 -> task14 [label="generated1-markdup.bam"];
    58    task1 -> task15 [label="e-coli-NC_011750.1.fasta.bwt"];
    59    task10 -> task15 [label="generated21-fix.fq.gz"];
    60    task11 -> task15 [label="generated22-fix.fq.gz"];
    61    task15 -> task16 [label="generated2.bam"];
    62    task2 -> task17 [label="e-coli-NC_011750.1.dict"];
    63    task16 -> task17 [label="generated2-markdup.bam"];
    64    task14 -> task18 [label="generated1-bqsr.txt"];
    65    task17 -> task18 [label="generated2-bqsr.txt"];
    66    task2 -> task19 [label="e-coli-NC_011750.1.dict"];
    67    task13 -> task19 [label="generated1-markdup.bam"];
    68    task18 -> task19 [label="generated-bqsr-merged.txt"];
    69    task2 -> task20 [label="e-coli-NC_011750.1.dict"];
    70    task16 -> task20 [label="generated2-markdup.bam"];
    71    task18 -> task20 [label="generated-bqsr-merged.txt"];
    72    task19 -> task21 [label="generated1-recal.bam"];
    73    task20 -> task21 [label="generated2-recal.bam"];
    74    task21 -> task22 [label="generated-merged.bam"];
    75    task2 -> task23 [label="e-coli-NC_011750.1.dict"];
    76    task21 -> task23 [label="generated-merged.bam"];
    77    task22 -> task23 [label="generated-merged.bam.bai"];
    78    task2 -> task24 [label="e-coli-NC_011750.1.dict"];
    79    task23 -> task24 [label="generated-call.vcf.gz"];
    80    output1 [label="generated1-markdup-metrics.txt", color=blue];
    81    task13 -> output1;
    82    output2 [label="generated-call-result.vcf.gz", color=blue];
    83    task24 -> output2;
    84    output3 [label="generated2-markdup-metrics.txt", color=blue];
    85    task16 -> output3;
    86    output4 [label="generated-merged-realigned.bam", color=blue];
    87    task23 -> output4;
    88  }
    89