Commit 18feccef authored by mbruno's avatar mbruno
Browse files

refactor(config): add a config file template

parent 3efb13f6
format: RAPIDRUN #or CLASSIC (required = TRUE)
resources:
job: 8
singularity:
ednatools: #path to ednatools.simg singularity image (required = FALSE)
obitools: #path to obitools.simg singularity image (required = FALSE)
fichiers:
rapidrun: #path to all_samples.csv (required = TRUE if format = RAPIDRUN)
folder_fastq: #path to fastq files (reuqired = TRUE)
dat:
mamm: #path to Mamm.dat
teleo: #path to Teleo.dat
chond: #path to Chond.dat
vert: #path to Vert.dat
blacklist: #blacklisted projects/run to exclude from the analysis (default = dummy_run)
projet:
- dummy_run
run:
- dummy_run
reference: #path to ecoPCR taxonomy Databases and to fasta file containing reference sequences
mamm:
prefix: embl_std
folder: resources/test/test_rapidrun_data/bdr/reference_database_mamm/
fasta: resources/test/test_rapidrun_data/bdr/reference_database_mamm/db_embl_std.fasta
teleo:
prefix: embl_std
folder: resources/test/test_rapidrun_data/bdr/reference_database_teleo/
fasta: resources/test/test_rapidrun_data/bdr/reference_database_teleo/db_embl_std.fasta
chond:
prefix: embl_std
folder: resources/test/test_rapidrun_data/bdr/reference_database_chond/
fasta: resources/test/test_rapidrun_data/bdr/reference_database_chond/db_embl_std.fasta
vert:
prefix: embl_std
folder: resources/test/test_rapidrun_data/bdr/reference_database_vert/
fasta: resources/test/test_rapidrun_data/bdr/reference_database_vert/db_embl_std.fasta
custom_baseref: FALSE #use custom reference database (required = TRUE, default = FALSE, type = boolean)
custom_ref: #(required = FALSE if custom_baseref = FALSE)
marker:
taxonomy_folder: #path to marker custom taxonomy
fasta: #path to marker custom fasta
fastqc: False #run control quality (required = TRUE, default = FALSE, type = boolean)
merge_fastq:
encoding: 33 #VSEARCH, FASTQ output quality score ASCII base char (required = TRUE, default = 33)
merging:
vsearch:
cores: 8 #VSEARCH, number of threads to use, zero for all cores (required = TRUE, default = 8)
demultiplexing:
maxLen: 120 #Cutadapt, Discard reads longer than LEN (required = TRUE, default = 120, type = int)
minLen: 20 #Cutadapt, Discard reads shorter than LEN (required = TRUE, default = 20, type = int)
job: 4 #Cutadapt, Number of CPU cores to use. Use 0 to auto-detect (required = TRUE, default = 4)
clustering:
swarm:
cores: 8 #Swarm, number of threads to use (required = TRUE, default = 8)
assignment:
ecotag:
minIdentity: 0.0 #minimum identity to consider (required = TRUE, default = 0.0, type = int)
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