Commit 2feb7312 authored by aknecht2's avatar aknecht2
Browse files

Added individual job yaml files.

parent c59ee118
from pymongo import MongoClient
def setup
bwa_align_paired:
inputs:
- fna
- fastq
- fastq
outputs:
- sam
arguments:
- "-M":
changeable: false
required: true
value: false
- "-t":
changeable: true
required: false
default: 1
value: true
- "$inputs.0":
changeable: false
required: true
value: false
- "$inputs.1":
changeable: false
required: true
value: false
- "$inputs.2":
changeable: false
required: true
value: false
walltime: 2000
memory: 2000
bwa_align_single:
inputs:
- fna
- fastq
outputs:
- sai
command: bwa
arguments:
- aln:
changeable: false
required: true
value: false
- "-q":
changeable: true
required: false
default: 5
value: true
- "-l":
changeable: true
required: false
default: 32
value: true
- "-k":
changeable: true
required: false
default: 2
value: true
- "-t":
changeable: true
required: false
default: 1
value: true
- "$inputs.0":
changeable: false
required: true
value: false
- "$inputs.1":
changeable: false
required: true
value: false
walltime: 2000
memory: 2000
bwa_sai_to_sam:
inputs:
- fna
- sai
- fastq
outputs:
- sam
command: bwa
arguments:
- samse:
changeable: false
required: true
value: false
- "$inputs.0":
changeable: false
required: true
value: false
- "$inputs.1":
changeable: false
required: true
value: false
- "$inputs.2":
changeable: false
required: true
value: false
walltime: 2000
memory: 2000
samtools_sam_to_bam:
inputs:
- sam
outputs:
- bam
arguments:
- view:
changeable: false
required: true
value: false
- "-bS"
changeable: false
required: true
value: false
- "$inputs.0"
changeable: false
required: true
value: false
walltime: 2000
memory: 2000
import sys
def progress(current, end):
def progress(current, end, length = 20):
percent = float(current) / end
hashes = "#" * int(round(percent * 20))
spaces = " " * (20 - len(hashes))
hashes = "#" * int(round(percent * length))
spaces = " " * (length - len(hashes))
sys.stdout.write("\rProcessed %s / %s entries. [%s] %s%%" % (current, end, hashes + spaces, int(round(percent * 100))))
sys.stdout.flush()
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