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Merge pull request #312 from jlac/master
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updated version of multiqc to v1.3
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@jlac
jlac committed Jan 10, 2018
2 parents 0234876 + a255617 commit c22456b
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Showing 13 changed files with 26 additions and 25 deletions.
2 changes: 1 addition & 1 deletion Rules/all-exomeseq-germline.rl
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Expand Up @@ -13,6 +13,6 @@ rule all_exomeseq_germline:
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-exomeseq-somatic-tumoronly.rl
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Expand Up @@ -22,7 +22,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""

Expand Down Expand Up @@ -50,7 +50,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""

Expand All @@ -77,6 +77,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-exomeseq-somatic.rl
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Expand Up @@ -44,7 +44,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
elif config['project']['annotation'] == "hg38":
Expand Down Expand Up @@ -93,7 +93,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""

Expand Down Expand Up @@ -139,6 +139,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-rnafusion.rl
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Expand Up @@ -35,7 +35,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; rm *featureCounts; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl
Scripts/fusionSummary.sh; module load multiqc/1.3; multiqc -f .; rm *featureCounts; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl

"""

Expand Down Expand Up @@ -76,7 +76,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl
Scripts/fusionSummary.sh; module load multiqc/1.3; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl

"""

Expand Down Expand Up @@ -113,6 +113,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl
Scripts/fusionSummary.sh; module load multiqc/1.3; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl

"""
2 changes: 1 addition & 1 deletion Rules/all-rnaseqvar-somatic.rl
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Expand Up @@ -41,6 +41,6 @@ rule all_exomeseq_somatic:
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""
2 changes: 1 addition & 1 deletion Rules/all-rnaseqvargerm.rl
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Expand Up @@ -14,6 +14,6 @@ rule all_rnaseqvargerm:
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; rm *sorted.bam.bai; mv *sorted.txt logfiles/; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; rm *sorted.bam.bai; mv *sorted.txt logfiles/; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-wgs-somatic-tumoronly.rl
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Expand Up @@ -21,7 +21,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
elif config['project']['annotation'] == "hg38":
Expand All @@ -47,7 +47,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""

Expand All @@ -72,6 +72,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-wgs-somatic.rl
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Expand Up @@ -45,7 +45,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
elif config['project']['annotation'] == "hg38":
Expand Down Expand Up @@ -95,7 +95,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""

Expand Down Expand Up @@ -142,6 +142,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/

"""
6 changes: 3 additions & 3 deletions Rules/all-wgslow.rl
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ if config['project']['annotation'] == "hg19":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""

Expand Down Expand Up @@ -100,7 +100,7 @@ elif config['project']['annotation'] == "hg38":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""

Expand Down Expand Up @@ -148,6 +148,6 @@ elif config['project']['annotation'] == "mm10":
output:
params: rname="final"
shell: """
module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/
module load multiqc/1.3; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/

"""
3 changes: 2 additions & 1 deletion Rules/gatk.realign.rl
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Expand Up @@ -7,4 +7,5 @@ rule gatk_realign:
sam=config['bin'][pfamily]['SAMTOOLS'],
picard3=config['bin'][pfamily]['PICARD3'],
knownindels=config['references'][pfamily]['KNOWNINDELS'],rname="pl:realign"
shell: "{params.sam} index {input};module load GATK/3.5-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T RealignerTargetCreator -I {input} -R {params.genome} {params.knownindels} -o {output.int}; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} {params.knownindels} -o {output.re}"
threads: 2
shell: "{params.sam} index {input};module load GATK/3.5-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T RealignerTargetCreator -I {input} -R {params.genome} {params.knownindels} -o {output.int} -nt 2; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} {params.knownindels} -o {output.re}"
2 changes: 1 addition & 1 deletion Rules/multiqc.rl
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Expand Up @@ -3,6 +3,6 @@ rule multiqc:
output: "multiqc_report.html"
params: fastqc=config['bin'][pfamily]['FASTQC'],adapters=config['references'][pfamily]['fastqc.adapters'],rname="pl:multiqc"
threads: 1
shell: "module load multiqc/1.1; multiqc -f -e featureCounts ."
shell: "module load multiqc/1.3; multiqc -f ."


2 changes: 1 addition & 1 deletion Rules/multiqc_genomeseq.rl
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Expand Up @@ -3,6 +3,6 @@ rule multiqc_genomeseq:
output: "multiqc_report.html"
params: fastqc=config['bin'][pfamily]['FASTQC'],adapters=config['references'][pfamily]['fastqc.adapters'],rname="pl:multiqc_genome"
threads: 1
shell: "module load multiqc/1.1; multiqc -f -e featureCounts ."
shell: "module load multiqc/1.3; multiqc -f ."


2 changes: 1 addition & 1 deletion cluster.json
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Expand Up @@ -545,7 +545,7 @@
},
"gatk_realign":
{
"threads": "1",
"threads": "2",
"gres":"lscratch:500",
"mem": "64g"
},
Expand Down

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