yakneens

def set_up_dag_run(context, dag_run_obj):
    dag_run_obj.payload = {"config": context["config"]}
    dag_run_obj.run_id = str(uuid4())
    print context
    return dag_run_obj
    
def launch_workflow_command(args):

    config_location = args.config_location
    analysis_id = args.analysis_id

yakneens

from airflow import DAG
from airflow.operators import BashOperator, PythonOperator
from datetime import datetime, timedelta
from sqlalchemy.ext.automap import automap_base
from sqlalchemy.orm import Session
from sqlalchemy import create_engine
from sqlalchemy import or_, and_
from os import system
# Commenting out full list of contigs for now leaving only 1-22, X, Y
#contig_names = ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT","GL000207.1","GL000226.1","GL000229.1","GL000231.1","GL000210.1","GL000239.1","GL000235.1","GL000201.1","GL000247.1","GL000245.1","GL000197.1","GL000203.1","GL000246.1","GL000249.1","GL000196.1","GL000248.1","GL000244.1","GL000238.1","GL000202.1","GL000234.1","GL000232.1","GL000206.1","GL000240.1","GL000236.1","GL000241.1","GL000243.1","GL000242.1","GL000230.1","GL000237.1","GL000233.1","GL000204.1","GL000198.1","GL000208.1","GL000191.1","GL000227.1","GL000228.1","GL000214.1","GL000221.1","GL000209.1","GL000218.1","GL0

yakneens

from airflow import DAG
from airflow.operators import BashOperator, PythonOperator
from datetime import datetime, timedelta
from sqlalchemy.ext.automap import automap_base
from sqlalchemy.orm import Session
from sqlalchemy import create_engine
from sqlalchemy import or_, and_
from os import system
# Commenting out full list of contigs for now leaving only 1-22, X, Y
#contig_names = ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT","GL000207.1","GL000226.1","GL000229.1","GL000231.1","GL000210.1","GL000239.1","GL000235.1","GL000201.1","GL000247.1","GL000245.1","GL000197.1","GL000203.1","GL000246.1","GL000249.1","GL000196.1","GL000248.1","GL000244.1","GL000238.1","GL000202.1","GL000234.1","GL000232.1","GL000206.1","GL000240.1","GL000236.1","GL000241.1","GL000243.1","GL000242.1","GL000230.1","GL000237.1","GL000233.1","GL000204.1","GL000198.1","GL000208.1","GL000191.1","GL000227.1","GL000228.1","GL000214.1","GL000221.1","GL000209.1","GL000218.1","GL0

yakneens

[root@genotyper-8 centos]# zcat /reference/genome.fa.gz | grep chromosome
>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
>2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
>3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
>4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
>5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
>6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
>7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
>8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
>9 dna:chromosome chromosome:GRCh37:9:1:141213431:1

yakneens

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	f8696c79-b162-92a6-e040-11ac0c4804bf
1	10004	.	T??@̨?? ??X焙D?V????4??ğ?]ګ??V???O??????N#???M?R2#MO?????KKFB??T???5??Y?HG?*?̤#R??K????	CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT	0	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=100X;DP=7;DPB=41.36;DPRA=0;EPP=0;EPPR=0;GTI=0;LEN=100;MEANALT=3;MQM=29;MQMR=0;NS=1;NUMALT=1;ODDS=52.6792;PAIRED=1;PAIREDR=0;PAO=66;PQA=862;PQR=0;PRO=0;QA=42;QR=0;RO=0;RPL=5;RPP=13.8677;RPPR=0;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=mnp;technology.ILLUMINA=1	GT:DP:RO:QR:AO:QA:GL	1/1:7:0:0:5:42:0
1	10123	.	T	C	0	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=119;CIGAR=1X;DP=120;DPB=120;DPRA=0;EPP=43.3194;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=20.0672;MQMR=0;NS=1;NUMALT=1;ODDS=69.9353;PAIRED=0.378151;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=852;QR=0;RO=0;RPL=105;RPP=154.119;RPPR=0;RPR=14;RUN=1;SAF=40;SAP=30.765;SAR=79;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:119:

yakneens

provider "aws" {
        access_key = "${var.access_key}"
        secret_key = "${var.secret_key}"
        region="${var.aws_region}"
}

resource "aws_security_group" "default" {
        name = "salt_master_sg"
        description = "Security group for the Salt Master Node"