Mercurial > repos > fubar > egapx_runner

comparison examples/input_D_farinae_minimal.yaml @ 0:d9c5c5b87fec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d9c5c5b87fec
1 # This is a very minimal example of EGAPx, it fits into 4 CPU cores and 6GB of memory.
2 # To be able to do this, we culled the input files and some stages of execution.
3 # To limit the requirements you also need to use -e docker_minimal
4
5 genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
6 reads:
7 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1
8 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2
9 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1
10 - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2
11 taxid: 6954
12 proteins: []
13 hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params
14 tasks:
15 star_wnode:
16 star_wnode: -cpus-per-worker 4