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Flowchart.txt
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Flowchart.txt
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# Copyright 2016 UCSC Computational Genomics Lab
# Original contributor: Arjun Arkal Rao
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
0
|
1
____________________|__________________
/ | | | | \
2--+ +-3 4-+ +--5 +--6 7--+
| | | | | | | |_|__|___| |
| | | |_____| | | | | |
8 \_ _ \_ _|_ _ _\_ _ _ _ _/_ _ /_ _| _ _ /|
| | _|_ | |
| | | 9 | | |
| | +---+ | |
____|____ _____|___________ | |
/ | \ / / / | \ \ | |
| | | | | | | | 10 |
11 12 13 14 15 16 17 | | |
| | | | | | | | | |
| | 18 19 20 | 21 22 | |
| | | | | | | | | |
| \_____\___\__|__/___/__ / | |
| | | |
| 23 | |
| | | |
| 24 | |
| \______________________/ |
|\_ _ _ _ _ _ _ _ _ _ _ _ _ _ _|_ _ _ _ _ _ _ _ _ __\_ _
| | _\__
| | | 25 |
| 26 +----+
| ____________|_____________
| / / \ \
| MIN MIT MIIN MIIT
| | | | |
| \_____\______________/_____/
| |
| 27
| _|__
+----------------------------| 28 |
+----+
0 = Launchpad
1 = Prepare sample (Download if necessary)
2 = Process RNA for Adapters (CUTADAPT)
3 = Align Tumor DNA (BWA)
4 = Align Normal DNA (BWA)
5 = Decipher MHC Haplotype Tumor DNA (PHLAT)
6 = Decipher MHC Haplotype Normal DNA (PHLAT)
7 = Decipher MHC Haplotype Tumor RNA (PHLAT)
8 = Align RNA (STAR)
9 = Delete Fastqs to cleanup space for future jobs
10 = Merge PHLAT outputs (PYTHON SCRIPT)
11 = Calculate Gene Expression (RSEM)
12 = Identify Fusion Genes (Star Fusion + Fusion Inspector)
*13 = Mutation Calling 1 (RADIA)
*14 = Mutation Calling 2 (Mutect)
*15 = Mutation Calling 3 (MuSE)
16 = Mutation Calling 4 (Strelka)
*17 = Mutation Calling 5 (SomaticSniper)
18 = Merge Mutation Calls 1 (RADIA)
19 = Merge Mutation Calls 2 (Mutect)
20 = Merge Mutation Calls 3 (MuSE)
21 = Merge Mutation Calls 4 (SomaticSniper)
22 = INDEL Calling (Strelka)
23 = translate to Protein space (SnpEff, Future Translator)
24 = Convert AA change to peptides (TRANSGENE)
25 = MHC Pathway assessment
+26 = Spawn mhci prediction on n mhci alleles (MI)
and mhcii prediction on m mhcii alleles (MII)
MIN = Predict normal peptides binding to n predicted MHCI alleles
MIT = Predict tumor peptides binding to n predicted MHCI alleles
MIIN = Predict normal peptides binding to n predicted MHCII alleles
MIIT = Predict tumor peptides binding to n predicted MHCII alleles
27 = merge MHC:peptide binding predictions
28 = Rank Boost
* = Nodes will dynamically spawn 1 child per input chromosome in input fai
+ = Nodes will dynamically spawn 1 child per predicted mhc (I and II)
Numbers in boxes represent terminal nodes of the DAG