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issue #196: Fix @RG tag in sam/bam file output #200

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issue #196: Fix @RG tag in sam/bam file output #200

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a70d7cc
issue_196: Build @RG ID tag - add lane to sample name if exists
kamyshova Apr 27, 2021
a6167cc
issue_196: Build @RG ID tag - add synthetic sample lane to sample name
kamyshova Apr 28, 2021
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2 changes: 1 addition & 1 deletion config/checkstyle/checkstyle.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@
<module name="IllegalInstantiation"/>
<module name="InnerAssignment"/>
<module name="MagicNumber">
<property name="ignoreNumbers" value="-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 256, 1024, 65535"/>
<property name="ignoreNumbers" value="-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 100, 256, 1024, 65535"/>
<property name="ignoreHashCodeMethod" value="true"/>
</module>
<module name="MissingSwitchDefault"/>
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2 changes: 1 addition & 1 deletion ...nalyses/gSingleDnaAmplicon/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...aAnalyses/gSingleDnaCapture/DnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...tureVarFastq/AllTasksPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...tureVarFastq/AllTasksSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...q/BwaPicardQcAbraGatkPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...q/BwaPicardQcAbraGatkSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...stq/BwaPicardQcTargetSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...alpelLofreqFreebayesPaired/dnaCaptureVar_Fastq_alignment_for_smv1_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion .../TrimmomaticNovoalignSingle/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...stq/XenomeSeqpurgeBwaPaired/dnaCaptureVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...ources/templates/DnaWgsVarFastq/DnaWgsVar_Fastq_alignment_for_GA5_1_analysis_template.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...q/testControlSampleAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...tControlSampleNotNAAllTasksXenomeNo/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...onVarFastq/testPairedPicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion ...astq/testPairedXenomeYesSeqpurgeBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...estPairedXenomeYesSeqpurgeNovoalign/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...q/testPairedXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...onVarFastq/testSinglePicardAbraGatk/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion ...q/testSingleXenomeYesTrimmomaticBwa/DnaAmpliconVar_Fastq_alignment_for_GA5_1_analysis.txt
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Expand Up @@ -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.
Expand Down
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