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Merge pull request #27 from SciDAP/master
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remove bam's files
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portah committed Nov 27, 2015
2 parents 96080cf + 757e3c2 commit 482668e
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20 changes: 20 additions & 0 deletions tools/jobs/realignTargetCreatorJob.json
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{

"inputBam_realign": {
"class": "File",
"path": "markDups.bam"
},
"reference": {
"class": "File",
"path": "./outputFiles/hg19.fa",
},
"jar_file": {
"class": "File",
"path": "GenomeAnalysisTK-2.8.jar",
},

"known": [{"class": "File", "path": "dbsnp_138.vcf"}, {"class": "File", "path": "../data//GATK-complete-workflow/Ref_datasets/Mills_and_1000G_gold_st.vcf"}, {"class": "File", "path": "../data//GATK-complete-workflow/Ref_datasets/1000G_phase1.indels.hg19.vcf"} ],

"outputfile_realignTarget": "realignTargetCreator_output.intervals"
}

8 changes: 8 additions & 0 deletions tools/jobs/samtools-rmdup-job.json
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{
"input": {
"class": "File",
"path": "./test-files/dna.SRR096326.bam"
},
"output_name": "dna.SRR096326.rmdup.bam",
"single_end": true
}
10 changes: 10 additions & 0 deletions tools/jobs/samtools-sort-job.json
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{
"input": {
"class": "File",
"path": "./test-files/rna.SRR948778.bam"
},
"compression_level": 9,
"memory": "1G",
"threads": 4,
"output_name": "./test-files/rna.SRR948778.sorted.bam"
}

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