update work log for gbm confirmatory samples

Author: caosgc33d

work_log_run_confirmatory_gbm_b1

@@ -39,3 +39,21 @@ perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmator
 
 perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4
 
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12
+
+perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13