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Commit 2e7bf5e2 authored by nicolas.fernandez_ird.fr's avatar nicolas.fernandez_ird.fr :shinto_shrine:
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v.2025.04

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config/config.yaml
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......@@ -97,7 +97,7 @@ reference: 'SARS-CoV-2_Wuhan_MN908947.3' # Your reference, in fasta format (defa
################################ SUBMISSIONS ##################################
###############################################################################
gisaid: ##TODO##
gisaid: # TODO
username: 'username'
threshold: '30'
name: 'hCoV-19'
......@@ -135,8 +135,8 @@ consensus:
max_depth: '0' # Max per-file depth; avoids excessive memory usage (default: '8000', recomanded "0") [INT]
# Passing zero for this option sets it to the highest possible value, effectively removing the depth limit.
min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
min_insert: '0' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
min_insert: '0.8' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
map_qual: '--no-BAQ' # Disable BAQ, per-Base Alignment Quality (default: '--no-BAQ')
# Available options, set only one:
......@@ -163,8 +163,8 @@ variant:
max_depth: '0' # Max per-file depth; avoids excessive memory usage (default: '8000', recomanded "0") [INT]
# Passing zero for this option sets it to the highest possible value, effectively removing the depth limit.
min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
min_insert: '0' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
min_insert: '0.8' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
map_qual: '--no-BAQ' # Disable BAQ, per-Base Alignment Quality (default: '--no-BAQ')
# Available options, set only one:
......@@ -175,37 +175,37 @@ variant:
min_qual: '0' # -q: Minimum quality score threshold to count base (Default: '20', recomanded: '0') [INT]
###############################################################################
############################# PRIMERS CLEAPING ###############################
############################# PRIMERS CLEAPING ################################
###############################################################################
primers:
offset: '0' # Offset for primer trimming (default: '0') [INT]
min_length: '35' # Minimum length of read to retain after trimming (Default: 50% average length of the first 1000 reads) [INT]
min_qual: '20' # Minimum quality threshold for sliding window to pass (Default: '20') [INT]
slide: '4' # Width of sliding window (Default: '4') [INT]
min_qual: '20' # Minimum quality threshold for sliding window to pass (Default: '20') [INT]
slide: '4' # Width of sliding window (Default: '4') [INT]
bed:
path: 'resources/primers_schemes/bed/' # Path to primers bed files (default 'resources/primer/bed') [PATH]
scheme: 'nCoV-2019/V4.1/SARS-CoV-2.primer.bed' # Your primer set, in BED format (no default: you need to know which kit and reference you used!)
scheme: # Your primer set, in BED format (you need to know which kit and reference you used!)
# Reference sequence names and coordinates of BAM and BED are assumed to be derived from identical reference sequences.
# Available options (not exhaustive), set only one:
##- 'nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V5.3.2 (latest)
##- 'nCoV-2019/V4.1/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
- 'nCoV-2019/V4.1/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
##- 'nCoV-2019/V4/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V4 (not based on V3, see Artic README)
##- 'nCoV-2019/V3/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V3
##- 'nCoV-2019/V2/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V2
##- 'nCoV-2019/V1/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V1
##- 'ZaireEbola/V3/ZaireEbola.primer.bed' # EBOV Artic V3
##- 'ZaireEbola/V2/ZaireEbola.primer.bed' # EBOV Artic V2 (based on AF272001.1)
##- 'ZaireEbola/V2/ZaireEbola.primer.bed' # EBOV Artic V2 (based on AF272001.1)
##- 'ZaireEbola/V1/ZaireEbola.primer.bed' # EBOV Artic V1
##- 'Nipah/V1/NiV_6_Malaysia.primer.bed' # NIV Artic V1
##- 'MPXV/V1/MPXV.primer.bed' # MPXV V1 (dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v4)
##- 'your_custom_amplicon_kit.bed' # Add your custom amplicon kit
bedpe:
path: 'resources/primers_schemes/bedpe/' # Path to primers bedpe files (default 'resources/primer/bedpe') [PATH]
scheme: #'insert_here' # Your primer set, in BEDPE format (no default: you need to know which kit and reference you used!)
scheme: # Your primer set, in BEDPE format (you need to know which kit and reference you used!)
# Reference sequence names and coordinates of BAM and BED are assumed to be derived from identical reference sequences.
# Available options (not exhaustive), set only one:
##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe' # SARS-CoV-2 Artic V4 (not based on V3, see Artic README)
##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe' # SARS-CoV-2 Artic V3
##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe' # SARS-CoV-2 Artic V2
......@@ -293,7 +293,7 @@ cutadapt:
############################### QUALITY CONTROL ###############################
###############################################################################
multiqc: ##TODO##
multiqc: # TODO
path: 'config/multiqc/' # Path to the multiqc configuration file
config: 'default.yaml' # Multiqc configuration file (default: default.yaml)
# Available options (not exhaustive), set only one:
......@@ -357,7 +357,7 @@ fastq_screen:
############################### RENAME SAMPLES ################################
###############################################################################
rename: ##TODO##
rename: # TODO
barcode_id: true
line_id: true
end_id: true
......
workflow/Snakefile
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− 2
View file @ 2e7bf5e2
......@@ -59,7 +59,7 @@ functions.MODULES = config["modules"] # Modules
functions.MAPPER = config["tools"]["mapper"] # Reads mapper ('bwa', 'minimap2' or 'bowtie2')
functions.CALLER = config["tools"]["caller"] # Variants caller ('ivar' or 'ivar')
functions.ASSIGNER = config["tools"]["assigner"] # Lineages assigner ('nextclade' or 'pangolin')
functions.REFERENCE = config["reference"] # Genome reference sequence, in fasta format
functions.REFERENCE = config["reference"] # Genome reference sequence, in fasta format
functions.MIN_DEPTH = config["consensus"]["min_depth"] # Minimum depth to call consensus, mark lower regions with 'N'
functions.QC_REF = config["fastq_screen"]["reference"] # FastqScreen config file genomes to index
functions.STAT_EXT = config["report"]["stat"]["extention"] # Stat reports extentions ('txt' 'tsv' 'json')
......@@ -100,7 +100,7 @@ SAMTOOLS = config["envs"]["samtools"] # SamTools conda environment
BEDTOOLS = config["envs"]["bedtools"] # BedTools conda environment
BAMCLIPPER = config["envs"]["bamclipper"] # BAMClipper onda environment
GAWK = config["envs"]["gawk"] # Awk (GNU) conda environment
IVAR = config["envs"] # iVar conda environment
IVAR = config["envs"]["ivar"] # iVar conda environment
TSV2VCF = config["envs"]["tsv2vcf"] # tsv2vcf conda environment
BCFTOOLS = config["envs"]["bcftools"] # BcfTools conda environment
PANGOLIN = config["envs"]["pangolin"] # Pangolin conda environment
......
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