diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml index 71cb5c89..4cd1aafa 100644 --- a/config/checkstyle/checkstyle.xml +++ b/config/checkstyle/checkstyle.xml @@ -81,7 +81,7 @@ - + diff --git a/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt index b4e5e4c6..cca3961b 100644 --- a/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 6b9a086a..4e026a77 100644 --- a/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index cacfd89e..4517e5ba 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 6b9a086a..4e026a77 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index cacfd89e..4517e5ba 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 6b9a086a..4e026a77 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 6b9a086a..4e026a77 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt index 75136c14..3e5996a4 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/BwaVardictMutect1Strelka2GatkHaplotypeCallerScalpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:smv1\tSM:smv1\tLB:DNA\tPL:Illumina" /ngs/data/demo/test/fastq/smv1_GTGTTCTA_L004_R1_001.fastq.gz /ngs/data/demo/test/fastq/smv1_GTGTTCTA_L004_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/smv1/bam/smv1_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:smv1_L001\tSM:smv1\tLB:smv1\tPL:Illumina" /ngs/data/demo/test/fastq/smv1_GTGTTCTA_L004_R1_001.fastq.gz /ngs/data/demo/test/fastq/smv1_GTGTTCTA_L004_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/smv1/bam/smv1_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 2e5fc27f..4167ca9e 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -33,7 +33,7 @@ else fi echo `date` Begin Step: Novoalign alignment... -/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $'@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina' -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted +/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $"@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 010a0875..8bd3321d 100644 --- a/src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaCaptureVarFastq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -49,7 +49,7 @@ else fi echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt b/src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt index 0397af94..cd71c554 100644 --- a/src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt +++ b/src/integrationTest/resources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: Novoalign alignment... -/ngs/data/tools/novoalign/v3.07.01/novoalign -c 8 -d /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.nix -o SAM $'@RG\tID:GA5\tSM:GA5\tLB:DNA\tPL:Illumina' -f /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /ngs/data/tools/samtools/v0.1.19/samtools view -bS -|/ngs/data/tools/samtools/v0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted +/ngs/data/tools/novoalign/v3.07.01/novoalign -c 8 -d /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.nix -o SAM $"@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" -f /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /ngs/data/tools/samtools/v0.1.19/samtools view -bS -|/ngs/data/tools/samtools/v0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index b4e5e4c6..cca3961b 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index 243e562c..c031b869 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index 243e562c..c031b869 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz /ngs/data/demo/test/fastq_data/GA5_0001_L002_R2_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index bc74bc97..c1985cb5 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -49,7 +49,7 @@ else fi echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index c416493a..e558efc3 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -49,7 +49,7 @@ else fi echo `date` Begin Step: Novoalign alignment... -/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $'@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina' -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz --amplicons /ngs/data/test_data_padded_decoy.txt --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted +/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $"@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz --amplicons /ngs/data/test_data_padded_decoy.txt --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index eeee92d9..93fcf1dc 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -51,7 +51,7 @@ else fi echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R2.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index 1fd3a1d0..286fe6db 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -19,7 +19,7 @@ cd build/resources/integrationTest/output echo `date` Begin the job execution... echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" /ngs/data/demo/test/fastq_data/GA5_0001_L002_R1_001.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index 32f07d96..58f1d1fa 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -48,7 +48,7 @@ else fi echo `date` Begin Step: BWA alignment... -/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted +/usr/bin/bwa mem -t 4 /ngs/data/reference_genome/hg19/hg19_decoy/hg19.decoy.fa -M -R "@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt index 5fc302a8..e50e4567 100644 --- a/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt +++ b/src/integrationTest/resources/templates/dnaAmpliconVarFastq/testSingleXenomeYesTrimmomaticNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt @@ -48,7 +48,7 @@ else fi echo `date` Begin Step: Novoalign alignment... -/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $'@RG\tID:GA5\tSM:GA5\tLB:GA5\tPL:Illumina' -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz --amplicons /ngs/data/test_data_padded_decoy.txt --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted +/usr/bin/novoalign -c 4 -d /ngs/data/novoindexDB/novoindex.nix -o SAM $"@RG\tID:GA5_L001\tSM:GA5\tLB:GA5\tPL:Illumina" -f build/resources/integrationTest/output/GA5/fastq/GA5_1.trimmed.R1.fastq.gz --amplicons /ngs/data/test_data_padded_decoy.txt --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| /opt/samtools/samtools-0.1.19/samtools view -bS -|/opt/samtools/samtools-0.1.19/samtools sort - build/resources/integrationTest/output/GA5/bam/GA5_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/main/java/com/epam/fonda/tools/impl/BwaSort.java b/src/main/java/com/epam/fonda/tools/impl/BwaSort.java index d0c8f3dc..465fae3d 100644 --- a/src/main/java/com/epam/fonda/tools/impl/BwaSort.java +++ b/src/main/java/com/epam/fonda/tools/impl/BwaSort.java @@ -1,5 +1,5 @@ /* - * Copyright 2017-2020 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) + * Copyright 2017-2021 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ import com.epam.fonda.tools.Tool; import com.epam.fonda.tools.results.BamOutput; import com.epam.fonda.tools.results.BamResult; -import com.epam.fonda.workflow.PipelineType; +import com.epam.fonda.utils.DnaUtils; import com.epam.fonda.workflow.TaskContainer; import lombok.AllArgsConstructor; import lombok.Data; @@ -35,6 +35,7 @@ import java.util.Arrays; import static com.epam.fonda.utils.ToolUtils.validate; +import static java.lang.String.format; @Data @AllArgsConstructor @@ -55,11 +56,11 @@ public class BwaSort implements Tool { */ @Override public BamResult generate(Configuration configuration, TemplateEngine templateEngine) { - BwaSortFields bwaSortFields = constructFieldsForBwaSort(configuration); if (fastq1 == null) { throw new IllegalArgumentException( "Error Step: In bwaSort: no fastq files are properly provided, please check!"); } + BwaSortFields bwaSortFields = constructFieldsForBwaSort(configuration); Context context = new Context(); context.setVariable("bwaSortFields", bwaSortFields); context.setVariable("fastq1", fastq1); @@ -71,7 +72,7 @@ public BamResult generate(Configuration configuration, TemplateEngine templateEn .build(); bamOutput.setBam(StringUtils.isBlank(bamOutput.getBam()) ? bwaSortFields.sortedBam - : String.format("%s,%s", bamOutput.getBam(), bwaSortFields.sortedBam)); + : format("%s,%s", bamOutput.getBam(), bwaSortFields.sortedBam)); AbstractCommand command = BashCommand.withTool(cmd); command.setTempDirs(Arrays.asList(bwaSortFields.sortedBam, bwaSortFields.sortedBamIndex)); TaskContainer.addTasks("BWA alignment", "Index bam"); @@ -95,21 +96,14 @@ private BwaSortFields constructFieldsForBwaSort(Configuration configuration) { bwaSortFields.fastq1 = fastq1; bwaSortFields.fastq2 = fastq2; bwaSortFields.sampleName = sample.getName(); - bwaSortFields.tmpBam = String.format("%s/%s_%d.bwa.sorted", + bwaSortFields.tmpBam = format("%s/%s_%d.bwa.sorted", bwaSortFields.sbamOutDir, bwaSortFields.sampleName, index); - bwaSortFields.sortedBam = String.format("%s.bam", bwaSortFields.tmpBam); - bwaSortFields.sortedBamIndex = String.format("%s.bai", bwaSortFields.sortedBam); - bwaSortFields.rg = constructFieldRG(configuration, sample.getName()); + bwaSortFields.sortedBam = format("%s.bam", bwaSortFields.tmpBam); + bwaSortFields.sortedBamIndex = format("%s.bai", bwaSortFields.sortedBam); + bwaSortFields.rg = DnaUtils.buildRGIdTag(sample.getName(), index); return bwaSortFields; } - private String constructFieldRG(Configuration configuration, String sampleName) { - return PipelineType.DNA_AMPLICON_VAR_FASTQ.getName() - .equals(configuration.getGlobalConfig().getPipelineInfo().getWorkflow()) - ? String.format("\"@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina\"", sampleName, sampleName, sampleName) - : String.format("\"@RG\\tID:%s\\tSM:%s\\tLB:DNA\\tPL:Illumina\"", sampleName, sampleName); - } - @Data private class BwaSortFields { private String bwa; diff --git a/src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java b/src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java index c7a8e786..7bdfed84 100644 --- a/src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java +++ b/src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java @@ -1,5 +1,5 @@ /* - * Copyright 2017-2020 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) + * Copyright 2017-2021 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -24,6 +24,7 @@ import com.epam.fonda.tools.Tool; import com.epam.fonda.tools.results.BamOutput; import com.epam.fonda.tools.results.BamResult; +import com.epam.fonda.utils.DnaUtils; import com.epam.fonda.workflow.PipelineType; import com.epam.fonda.workflow.TaskContainer; import lombok.AllArgsConstructor; @@ -35,6 +36,7 @@ import java.util.Arrays; import static com.epam.fonda.utils.ToolUtils.validate; +import static java.lang.String.format; @Data @AllArgsConstructor @@ -55,11 +57,11 @@ public class NovoalignSort implements Tool { */ @Override public BamResult generate(Configuration configuration, TemplateEngine templateEngine) { - NovoalignSortFields novoalignSortFields = constructFieldsForNovoalignSort(configuration); if (StringUtils.isBlank(fastq1)) { throw new IllegalArgumentException( "Error Step: In novoalignSort: no fastq files are properly provided, please check!"); } + NovoalignSortFields novoalignSortFields = constructFieldsForNovoalignSort(configuration); Context context = new Context(); context.setVariable("novoalignSortFields", novoalignSortFields); context.setVariable("fastq1", fastq1); @@ -72,7 +74,7 @@ public BamResult generate(Configuration configuration, TemplateEngine templateEn .build(); bamOutput.setBam(StringUtils.isBlank(bamOutput.getBam()) ? novoalignSortFields.sortedBam - : String.format("%s,%s", bamOutput.getBam(), novoalignSortFields.sortedBam)); + : format("%s,%s", bamOutput.getBam(), novoalignSortFields.sortedBam)); AbstractCommand command = BashCommand.withTool(cmd); command.setTempDirs(Arrays.asList(novoalignSortFields.sortedBam, novoalignSortFields.sortedBamIndex)); return BamResult.builder() @@ -95,15 +97,15 @@ private NovoalignSortFields constructFieldsForNovoalignSort(Configuration config novoalignSortFields.sampleName = sample.getName(); novoalignSortFields.numThreads = configuration.getGlobalConfig().getQueueParameters().getNumThreads(); novoalignSortFields.index = index; - novoalignSortFields.tmpBam = String.format("%s/%s_%s.novoalign.sorted", + novoalignSortFields.tmpBam = format("%s/%s_%s.novoalign.sorted", novoalignSortFields.getBamOutdir(), novoalignSortFields.getSampleName(), novoalignSortFields.getIndex()); - novoalignSortFields.sortedBam = String.format("%s.bam", + novoalignSortFields.sortedBam = format("%s.bam", novoalignSortFields.getTmpBam()); - novoalignSortFields.sortedBamIndex = String.format("%s.bai", + novoalignSortFields.sortedBamIndex = format("%s.bai", novoalignSortFields.getSortedBam()); - novoalignSortFields.rg = constructFieldRG(configuration, sample.getName()); + novoalignSortFields.rg = DnaUtils.buildRGIdTag(sample.getName(), index); return novoalignSortFields; } @@ -113,12 +115,6 @@ private String constructFieldBedPrimer(Configuration configuration) { : null; } - private String constructFieldRG(Configuration configuration, String sampleName) { - return isDnaAmpliconWorkflow(configuration) - ? String.format("\'@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina\'", sampleName, sampleName, sampleName) - : String.format("\'@RG\\tID:%s\\tSM:%s\\tLB:DNA\\tPL:Illumina\'", sampleName, sampleName); - } - private boolean isDnaAmpliconWorkflow(final Configuration configuration) { return PipelineType.DNA_AMPLICON_VAR_FASTQ.getName() .equals(configuration.getGlobalConfig().getPipelineInfo().getWorkflow()); diff --git a/src/main/java/com/epam/fonda/utils/DnaUtils.java b/src/main/java/com/epam/fonda/utils/DnaUtils.java index 8397fe32..8daa603e 100644 --- a/src/main/java/com/epam/fonda/utils/DnaUtils.java +++ b/src/main/java/com/epam/fonda/utils/DnaUtils.java @@ -1,5 +1,5 @@ /* - * Copyright 2017-2020 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) + * Copyright 2017-2021 Sanofi and EPAM Systems, Inc. (https://www.epam.com/) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -156,6 +156,17 @@ public static boolean isWgsWorkflow(final Configuration configuration) { return configuration.getGlobalConfig().getPipelineInfo().getWorkflow().toLowerCase().contains("wgs"); } + /** + * Build @RG ID tag - add lane to sample name + * @param sampleName + * @param index synthetic sample lane + * @return @RG ID tag + */ + public static String buildRGIdTag(final String sampleName, final int index) { + final String rgId = format("%s_L%s%s%s", sampleName, index / 100 % 10, index / 10 % 10, index % 10); + return format("\"@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina\"", rgId, sampleName, sampleName); + } + private static String getLogFileScanningShellScript(LogFileFields logFileFields, String tag, Map msgMap, Integer period, String index) { return TEMPLATE_ENGINE.process(LOGFILE_SCANNING_SHELL_SCRIPT_TEMPLATE_NAME, buildContext(logFileFields, diff --git a/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1.txt b/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1.txt index 6add7ee9..a127e4dd 100644 --- a/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1.txt +++ b/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: BWA alignment... -bwa mem -t 4 genome -M -R "@RG\tID:sampleName\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted +bwa mem -t 4 genome -M -R "@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt b/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt index 9e8d9cff..ce7c5540 100644 --- a/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt +++ b/src/test/resources/templates/ampliconBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: BWA alignment... -bwa mem -t 4 genome -M -R "@RG\tID:sampleName\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1 fastq2| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted +bwa mem -t 4 genome -M -R "@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1 fastq2| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1.txt b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1.txt index ab5f0463..c59e115d 100644 --- a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1.txt +++ b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:sampleName\tPL:Illumina' -f fastq1 --amplicons bedprimer --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 --amplicons bedprimer --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt index c3841288..b9c0cc53 100644 --- a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt +++ b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:sampleName\tPL:Illumina' -f fastq1 fastq2 --amplicons bedprimer --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 fastq2 --amplicons bedprimer --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2_without_bedprimer.txt b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2_without_bedprimer.txt index 34e587bb..4ce0cfb1 100644 --- a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2_without_bedprimer.txt +++ b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2_without_bedprimer.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina' -f fastq1 fastq2 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 fastq2 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_without_bedprimer.txt b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_without_bedprimer.txt index cfd61b95..3a1f118a 100644 --- a/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_without_bedprimer.txt +++ b/src/test/resources/templates/amplicon_novoalign_sort_test_tool_test_input_data_with_fastq1_without_bedprimer.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina' -f fastq1 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1.txt b/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1.txt index 6aa42340..a127e4dd 100644 --- a/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1.txt +++ b/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: BWA alignment... -bwa mem -t 4 genome -M -R "@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina" fastq1| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted +bwa mem -t 4 genome -M -R "@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt b/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt index 31cba8a2..ce7c5540 100644 --- a/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt +++ b/src/test/resources/templates/captureBwaSortTest_tool_test_input_data_with_fastq1_and_fastq2.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: BWA alignment... -bwa mem -t 4 genome -M -R "@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina" fastq1 fastq2| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted +bwa mem -t 4 genome -M -R "@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" fastq1 fastq2| samTools view -bS -|samTools sort - sbamOutdir/sampleName_1.bwa.sorted if [ $? -eq 0 ] then echo `date` Successful Step: BWA alignment. diff --git a/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1.txt b/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1.txt index cfd61b95..3a1f118a 100644 --- a/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1.txt +++ b/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina' -f fastq1 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment. diff --git a/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt b/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt index 34e587bb..4ce0cfb1 100644 --- a/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt +++ b/src/test/resources/templates/capture_novoalign_sort_test_tool_test_input_data_with_fastq1_and_fastq2.txt @@ -1,5 +1,5 @@ echo `date` Begin Step: Novoalign alignment... -novoalign -c 5 -d novoindex -o SAM $'@RG\tID:sampleName\tSM:sampleName\tLB:DNA\tPL:Illumina' -f fastq1 fastq2 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted +novoalign -c 5 -d novoindex -o SAM $"@RG\tID:sampleName_L001\tSM:sampleName\tLB:sampleName\tPL:Illumina" -f fastq1 fastq2 --hlimit 9 -t 0,2 -x 3 -H 22 --softclip 35 --trim3hp --matchreward 3 -k| samtools view -bS -|samtools sort - sbamOutdir/sampleName_1.novoalign.sorted if [ $? -eq 0 ] then echo `date` Successful Step: Novoalign alignment.