-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathnextflow.config
72 lines (57 loc) · 3.58 KB
/
nextflow.config
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
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
params {
outdir = "/hps/nobackup/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_v6"
dummy_fasta = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/dummy.fasta"
empty_file = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/EMPTY.txt"
pipeline_version = "6"
publish_dir_mode = 'copy'
generate_amplicon_db = false
generate_uniref90_db = false
silva_version = "138.1"
silva_download_taxdump = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2024-01-01.zip"
silva_ssu_label = "SILVA-SSU"
silva_ssu_download_fasta = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/SILVA_${silva_version}_SSURef_tax_silva_trunc.fasta.gz"
silva_ssu_download_taxmap = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/taxmap_slv_ssu_ref_${silva_version}.txt.gz"
silva_lsu_label = "SILVA-LSU"
silva_lsu_download_fasta = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/SILVA_${silva_version}_LSURef_tax_silva_trunc.fasta.gz"
silva_lsu_download_taxmap = "https://www.arb-silva.de/fileadmin/silva_databases/release_${silva_version}/Exports/taxmap_slv_lsu_ref_${silva_version}.txt.gz"
pr2_version = "5.0.0"
pr2_label = "PR2"
pr2_download_fasta = "https://github.com/pr2database/pr2database/releases/download/v${pr2_version}/pr2_version_${pr2_version}_SSU_mothur.fasta.gz"
pr2_download_tax = "https://github.com/pr2database/pr2database/releases/download/v${pr2_version}/pr2_version_${pr2_version}_SSU_mothur.tax.gz"
pr2_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/pr2_tax_header.txt"
unite_version = "9.0"
unite_label = "UNITE"
unite_repo_url = "https://doi.plutof.ut.ee/doi/10.15156/BIO/2483926"
unite_download_fasta = "https://files.plutof.ut.ee/public/orig/1A/C1/1AC1288ECCCC67B566050AEEF93A8CC298337B408A24C3E49E17ED28A33AE1BB.gz"
unite_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/unite_tax_header.txt"
rfam_version = "14.10"
rfam_label = "RFAM"
rfam_claninfo = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/temp_ribo.claninfo"
rfam_download_cm = "https://ftp.ebi.ac.uk/pub/databases/Rfam/${rfam_version}/Rfam.cm.gz"
itsonedb_version = "1.141"
itsonedb_label = "ITSone"
itsonedb_download_fasta = "https://itsonedb.cloud.ba.infn.it/ExportController?dbexport=ENA"
itsonedb_download_taxdump = "https://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip"
itsonedb_tax_header = "/hps/software/users/rdf/metagenomics/service-team/users/chrisata/taxdb_generation_nf/assets/itsonedb_tax_header.txt"
uniref90_version = "2024_05"
rheadb_version = "135"
uniprotKB_access_date = "2024-07-31"
uniref90_download_fasta = "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
rhea_chebi_download_mapping = "ftp://ftp.expasy.org/databases/rhea/txt/rhea-reactions.txt.gz"
uniprot_rhea_mapping = ""
uniref90_batch_size = 1000000
}
profiles {
standard {
includeConfig 'configs/local.config'
}
slurm {
includeConfig "configs/slurm.config"
process.executor = "slurm"
}
test_local {
includeConfig 'configs/test_local.config'
}
}
includeConfig 'configs/modules.config'
includeConfig 'configs/base.config'