config.yaml 898 Bytes
Newer Older
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
snakefiles:
  metaphlan3: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan3/metaphlan/paired/Snakefile
  metaphlan2_merge: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
  sample2markers: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/strainphlan/sample2markers/Snakefile
  strainphlan: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/strainphlan/strainphlan/Snakefile

samples:
  - sample_1
  - sample_2
  - sample_2

input_dir: /a/path/to/input/data
output_dir: output

metaphlan3:
  threads: 4
  input_type: fastq
  options: --bowtie2db /pasteur/zeus/projets/p02/metasig/DBs/metaphlan/metaphlan3bowtie2db/ --index mpa_v30_CHOCOPhlAn_201901

metaphlan2_merge:
  threads: 1

sample2markers:
  threads: 4

strainphlan:
  threads: 8
  options: ""
  clades:
    - s__Escherichia_coli
    - s__Klebsiella_pneumoniae