Merge pull request #27 from SciDAP/master

remove bam's files

Author: portah

tools/jobs/realignTargetCreatorJob.json

@@ -0,0 +1,20 @@
+{ 
+
+     "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" 
+}
+

tools/jobs/samtools-rmdup-job.json

@@ -0,0 +1,8 @@
+{
+    "input": {
+        "class": "File",
+        "path": "./test-files/dna.SRR096326.bam"
+    },
+    "output_name": "dna.SRR096326.rmdup.bam",
+    "single_end": true
+}

tools/jobs/samtools-sort-job.json

@@ -0,0 +1,10 @@
+{
+    "input": {
+        "class": "File",
+        "path": "./test-files/rna.SRR948778.bam"
+    },
+    "compression_level": 9,
+    "memory": "1G",
+    "threads": 4,
+    "output_name": "./test-files/rna.SRR948778.sorted.bam"
+}