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challenge.yaml
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challenge.yaml
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version: 1.0.0
arguments:
reads:
- format: bioboxes.org:/fastq
path: /exchange/input/Low_toy/S_S001__genomes_30__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Low/RL_S001__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium_toy/M1_S001__insert_5000_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium_toy/M1_S002__insert_5000_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium_toy/M2_S001__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium_toy/M2_S002__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium/RM1_S001__insert_5000.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium/RM1_S002__insert_5000.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium/RM2_S001__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/Medium/RM2_S002__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High_toy/H_S001__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High_toy/H_S002__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High_toy/H_S003__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High_toy/H_S004__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High_toy/H_S005__insert_180_reads_anonymous.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High/RH_S001__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High/RH_S002__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High/RH_S003__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High/RH_S004__insert_270.fq.gz
- format: bioboxes.org:/fastq
path: /exchange/input/High/RH_S005__insert_270.fq.gz
databases:
taxonomy:
path: ${PREFIX}/share/taxonomy/
format: bioboxes.org:/taxonomy_ncbi_dumps
metacv:
path: /exchange/db/
format: unknown
#download from https://s3-eu-west-1.amazonaws.com/cami-public-databases/metacv.tar.gz
#the program is looking for files containing the prefix "cvk6_2059".
#Contents should look like
# cvk6_2059.anno2inf
# cvk6_2059.cnt
# cvk6_2059.cor
# cvk6_2059.gis
# cvk6_2059.idmap
# cvk6_2059.inf
# cvk6_2059.ko2path
# cvk6_2059.wit
commonkmers:
path: /exchange/db/
format: unknown
#download from https://s3-eu-west-1.amazonaws.com/cami-public-databases/commonKmersData.tar.gz
#Contents should look like
# Bcalms
# CommonKmerMatrix-30mers.h5
# CommonKmerMatrix-50mers.h5
# FileNames.txt
# Info.txt
# Taxonomy.txt
taxypro:
path: /home/DB/Pfam27/
format: unknown
#download from https://s3-eu-west-1.amazonaws.com/cami-public-databases/taxypro.tar.gz
cache: /cache