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Commit 5d2f61d9 authored by nicolas.fernandez_ird.fr's avatar nicolas.fernandez_ird.fr :shinto_shrine:
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v.2025.03

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......@@ -13,7 +13,7 @@
# Version ________________ v.2025.03
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Bash script running gevarli.smk snakefile
# Aim ____________________ Bash script running GeVarLi snakefile
# Date ___________________ 2021.10.12
# Latest modifications ___ 2025.03.12
# Use ____________________ '. Run_GeVarLi.sh'
......@@ -24,55 +24,19 @@
#############
workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd) # Get working directory
version=$(<${workdir}/version.txt) # Get version
test_dir=$(<${workdir}/.test/) # Get test directory
###############################################################################
### OPERATING SYSTEM ###
########################
shell=$SHELL # Get shell
# Get operating system
case "$OSTYPE" in
darwin*) os="osx" ;;
linux*) os="linux" ;;
bsd*) os="bsd" ;;
solaris*) os="solaris" ;;
msys*) os="windows" ;;
cygwin*) os="windows" ;;
*) os="unknown (${OSTYPE})" ;;
esac
###############################################################################
### HARDWARE ###
################
if [[ ${os} == "osx" ]]
then
model_name=$(sysctl -n machdep.cpu.brand_string) # Get chip model name
physical_cpu=$(sysctl -n hw.physicalcpu) # Get physical cpu
logical_cpu=$(sysctl -n hw.logicalcpu) # Get logical cpu
mem_size=$(sysctl -n hw.memsize) # Get memory size (bit)
ram_gb=$(expr ${mem_size} \/ $((1024**3))) # mem_size / 1024**3 = Gb
elif [[ ${os} == "linux" || ${os} == "bsd" || ${os} == "solaris" ]]
then
model_name=$(lscpu | grep -o -E "Model name: +.+" | sed -E "s/Model name: +//") # Get chip model name
physical_cpu=$(lscpu | grep -o -E "^CPU\(s\): +[0-9]+" | sed -E "s/CPU\(s\): +//") # Get physical cpu
threads_cpu=$(lscpu | grep -o -E "^Thread\(s\) per core: +[0-9]+" | sed -E "s/Thread\(s\) per core: +//") # Get thread(s) per core
logical_cpu=$(expr ${physical_cpu} \* ${threads_cpu}) # Calcul logical cpu
mem_size=$(grep -o -E "MemTotal: +[0-9]+" /proc/meminfo | sed -E "s/MemTotal: +//") # Get memory size (Kb)
ram_gb=$(expr ${mem_size} \/ $((1024**2))) # mem_size / 1024**2 = Gb
else
echo -e "Please, use an '${ylo}UNIX${nc}' operating system, like: '${red}linux${nc}', '${red}osx${nc}' or '${red}WSL${nc}'."
return 0
fi
version=$(<${workdir}/VERSION_temp.txt) # Get version
blue="\033[1;34m" # blue
green="\033[1;32m" # green
red="\033[1;31m" # red
ylo="\033[1;33m" # yellow
nc="\033[0m" # no color
###############################################################################
### Network ###
### NETWORK ###
###############
# Test if network is online
if ping -c 1 -W 5 google.com > /dev/null 2>&1 || \
ping -c 1 -W 5 cloudflare.com > /dev/null 2>&1
then
......@@ -81,7 +45,6 @@ else
network="Offline"
fi
###############################################################################
### CONDA ###
#############
......@@ -89,29 +52,46 @@ fi
# Test if a conda distribution already exist
if [[ ! $(command -v conda) ]]
then # If no, invitation message to install it
message_conda="
echo -e "
${red}No Conda distribution found.${nc}
${blue}GeVarLi${nc} use the free and open-source package manager ${ylo}Conda${nc}.
Read documentation at: ${green}https://transvihmi.pages.ird.fr/nfernandez/GeVarLi/en/pages/installations/${nc}"
else # If yes, informations message about it
message_conda="
$(conda --version)
$(which conda)
$(conda config --show channels)"
fi
# Intern shell source conda
source ~/miniforge3/etc/profile.d/conda.sh 2> /dev/null # local user with miniforge3
source ~/mambaforge/etc/profile.d/conda.sh 2> /dev/null # local user with mambaforge ¡ Deprecated !
source ~/miniconda3/etc/profile.d/conda.sh 2> /dev/null # local user with miniconda3 ¡ Deprecated !
source /usr/local/bioinfo/miniconda3-23.10.0-1/etc/profile.d/conda.sh 2> /dev/null # iTROP HPC server (conda 23.11.0)
return 0
else # If yes, intern shell source conda
echo -e "\n ${green}Conda${nc} distribution found and sourced."
source ~/miniforge3/etc/profile.d/conda.sh 2> /dev/null # local user with miniforge3
source ~/mambaforge/etc/profile.d/conda.sh 2> /dev/null # local user with mambaforge ¡ Deprecated !
source ~/miniconda3/etc/profile.d/conda.sh 2> /dev/null # local user with miniconda3 ¡ Deprecated !
source /usr/local/bioinfo/miniconda3-23.10.0-1/etc/profile.d/conda.sh 2> /dev/null # iTROP HPC server (conda 23.11.0)
###############################################################################
### SPINNER ###
###############
bash ${workdir}/workflow/scripts/spinner2.sh > /dev/null 2>&1
# Function to run a command with a spinner
run_with_spinner() {
("$@" > /dev/null 2>&1) &
local pid=$!
disown $pid 2>/dev/null
local spinner=( "⠋" "⠙" "⠹" "⠸" "⠼" "⠴" "⠦" "⠧" "⠇" "⠏" )
local i=0
while kill -0 $pid 2>/dev/null; do
# Clear the line
printf "\r\033[K%s Please wait" "${spinner[$i]}"
i=$(( (i+1) % ${#spinner[@]} ))
sleep 0.1
done
wait $pid
local exit_code=$?
# Clear the spinner line
printf "\r\033[K"
if [ $exit_code -eq 0 ]; then
echo "✔ Job done!"
else
echo "✖ Job failed with exit code $exit_code."
fi
}
###############################################################################
### WORKFLOW-CORE ###
......@@ -120,278 +100,91 @@ bash ${workdir}/workflow/scripts/spinner2.sh > /dev/null 2>&1
# Test if 'workflow-core' environment exist.
if conda env list | grep -q "^workflow-core"
then # If 'exist'
echo -e "
${ylo}Workflow-Core${nc} conda environment already created.
"
if [[ $network == "Online" ]]
then # If 'online'
echo -e "\r
Updating ${ylo}Workflow-Core${nc} environment.
"
#run_with_spinner \
conda env update \
--prune \
--name workflow-core \
--file ${workdir}/workflow/envs/workflow-core.yaml
#> /dev/null 2>&1
echo -e "\n ${ylo}Workflow-Core${nc} conda environment already created."
# Test if 'workflow-core' environment is up-to-date.
ENV_YAML="${workdir}/workflow/envs/workflow-core.yaml"
CURRENT_ENV=$(conda env export --no-builds --name workflow-core | grep -v '^prefix:')
EXPECTED_ENV=$(grep -v '^prefix:' "$ENV_YAML")
if false #diff <(echo "$CURRENT_ENV") <(echo "$EXPECTED_ENV") > /dev/null
then # If 'up-to-date'
echo -e "\n ${ylo}Workflow-Core${nc} environment is already up-to-date."
else # If 'not' up-to-date
if [[ $network == "Offline" ]]
then # If 'offline'
echo -e "\n Cannot update ${ylo}Workflow-Core${nc} environment.
${green}Network${nc}: ${red}${network}${nc}."
else # If 'online'
echo -e "\n Updating ${ylo}Workflow-Core${nc} environment. \n"
run_with_spinner \
conda env update \
--prune \
--name workflow-core \
--file $ENV_YAML
fi
fi
else # If 'not' exist
echo -e "
${ylo}Workflow-Core${nc} conda environment not found.
"
echo -e "\n ${ylo}Workflow-Core${nc} conda environment not found."
if [[ $network == "Online" ]]
then # If 'online'
echo -e "
${ylo}Workflow-Core${nc} conda environment will be create, with:
echo -e "\n ${ylo}Workflow-Core${nc} conda environment will be create, with:
> ${red}Snakemake${nc}
> ${red}Snakedeploy${nc}
> ${red}Snakemake Slurm plugin${nc}
"
#run_with_spinner \
conda env create \
--file ${workdir}/workflow/envs/workflow-core.yaml \
--quiet \
> /dev/null 2>&1
> ${red}Snakemake Slurm plugin${nc} \n"
run_with_spinner \
conda env create \
--file ${workdir}/workflow/envs/workflow-core.yaml \
--quiet
else # If 'offline'
echo -e "\n Cannot install ${ylo}Workflow-Core${nc} environment.
${green}Network${nc}: ${red}${network}${nc}".
fi
fi
###############################################################################
### ACTIVATE WORKFLOW-CORE ###
###############################
# Active workflow-core conda environment.
if conda env list | grep -q "^workflow-core"
then
echo -e "\n Activate ${ylo}Workflow-Core${nc} conda environment."
conda activate workflow-core
else
echo -e "
${ylo}Workflow-Core${nc} conda environment not installed.
"
return 0
fi
###############################################################################
### CHECK CONFIGURATION ###
###########################
conda_version=$(conda --version | sed 's/conda //') # Conda version
mamba_version=$(mamba --version | head -n 1 | sed 's/mamba //') # Mamba version
snakemake_version=$(snakemake --version) # Snakemake version
config_file="${workdir}/config/config.yaml" # Get configuration file
fastq_dir=$(yq -Mr '.fastq_dir' ${config_file}) # Get path to fastq files directory
fastq_files=$(/bin/ls -l ${fastq_dir}/*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get fastq.gz files count
fastq_R1=$(/bin/ls -l ${fastq_dir}/*R1*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R1 fastq files count
fastq_R2=$(/bin/ls -l ${fastq_dir}/*R2*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R2 fastq files count
max_threads=$(yq -Mr '.resources.cpus' ${config_file}) # Get user config: max threads
max_memory=$(yq -Mr '.resources.ram' ${config_file}) # Get user config: max memory (Gb)
qualities=$(yq -Mr '.modules.qualities' ${config_file}) # Reads QC
keeptrim=$(yq -Mr '.modules.keeptrim' ${config_file}) # Keep trimmed reads
cleapping=$(yq -Mr '.modules.cleapping' ${config_file}) # Reads cleapping
covstats=$(yq -Mr '.modules.covstats' ${config_file}) # Mapping coverage stats
consensus=$(yq -Mr '.modules.consensus' ${config_file}) # Consensus
lineages=$(yq -Mr '.modules.lineages' ${config_file}) # Lineages assignation
gisaid=$(yq -Mr '.modules.gisaid' ${config_file}) # Gisaid submission file
# Get user config: genome reference
reference=$(yq -Mc '.consensus.reference' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: mapper
mapper=$(yq -Mc '.consensus.mapper' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: minimum coverage
min_cov=$(yq -Mc '.consensus.min_cov' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: minimum allele frequency
min_freq=$(yq -Mr '.consensus.min_freq' ${config_file})
# Get user config: assigner tool
assigner=$(yq -Mc '.consensus.assigner' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: hard clipping option
hard_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
# Get user config: dataset for nextclade
nextclade_dataset=$(yq -Mc '.nextclade.dataset' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//')
# Get user config: fastq_screen subsetption
fastqscreen_subset=$(yq -Mr '.fastq_screen.subset' ${config_file})
# Get user config: cutadapt clipping
cutadapt_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
###############################################################################
### MESSAGE ###
###############
# Timer
time_stamp_start=$(date +"%Y-%m-%d %H:%M") # Get system: analyzes starting time
time_stamp_archive=$(date +"%Y-%m-%d_%Hh%M") # Convert time for archive (wo space)
SECONDS=0 # Initialize SECONDS counter
# Colors
blue="\033[1;34m" # blue
green="\033[1;32m" # green
red="\033[1;31m" # red
ylo="\033[1;33m" # yellow
nc="\033[0m" # no color
# Message
message="
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}ABOUT${nc} ${blue}#####${nc}
${blue}-----------------${nc}
${green}Name${nc} ___________________ Run_GeVarLi.sh
${green}Version${nc} ________________ ${ylo}${version}${nc}
${green}Author${nc} _________________ Nicolas Fernandez
${green}Affiliation${nc} ____________ IRD_U233_TransVIHMI
${green}Aim${nc} ____________________ Bash script running GeVarLi Snakefile
${green}Date${nc} ___________________ 2021.10.12
${green}Latest modifications${nc} ___ 2025.03.12
${green}Use${nc} ____________________ '${ylo}. Run_GeVarLi.sh${nc}'
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Operating System${nc} ${blue}#####${nc}
${blue}----------------------------${nc}
${green}Shell${nc} __________________ ${ylo}${shell}${nc}
${green}Operating system${nc} _______ ${red}${os}${nc}
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Hardware${nc} ${blue}#####${nc}
${blue}--------------------${nc}
${ylo}Brand(R)${nc} | ${ylo}Type(R)${nc} | ${ylo}Model${nc} | ${ylo}@ Speed GHz${nc}
${green}Chip Model Name${nc} ________ ${model_name}
${green}Physical CPUs${nc} __________ ${red}${physical_cpu}${nc}
${green}Logical CPUs${nc} ___________ ${red}${logical_cpu}${nc} threads
${green}System Memory${nc} __________ ${red}${ram_gb}${nc} Gb of RAM
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Network${nc} ${blue}#####${nc}
${blue}-------------------${nc}
${green}Network${nc} ________________ ${red}${network}${nc}
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Conda${nc} ${blue}#####${nc}
${blue}-----------------${nc}
${message_conda}
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Workflow-Core${nc} ${blue}#####${nc}
${blue}-------------------------${nc}
${green}GeVarLi${nc} use ${green}Snakemake${nc}, a workflow manager.
${green}Snakemake${nc} is provided into ${red}Workflow-Core${nc}, a ${green}Conda${nc} environment.
You can remove old depreciated environements such as: 'gevarli-base', 'snakemake-base' or 'workflow-base'.
To list all your conda environments, you can run: '${ylo}conda env list${nc}'.
To remove old conda environments, you can run: '${ylo}conda remove --all --yes --name${nc} ${red}<ENV_NAME>${nc}'.
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Configuration${nc} ${blue}#####${nc}
${blue}-------------------------${nc}
${green}Starting time${nc} ______________ ${time_stamp_start}
${green}Conda version${nc} ______________ ${ylo}${conda_version}${nc}
${green}Mamba version${nc} ______________ ${ylo}${mamba_version}${nc}
${green}Snakemake version${nc} __________ ${ylo}${snakemake_version}${nc}
${green}Max threads${nc} ________________ ${red}${max_threads}${nc} of ${ylo}${logical_cpu}${nc} threads available
${green}Max memory${nc} _________________ ${red}${max_memory}${nc} of ${ylo}${ram_gb}${nc} Gb available
${green}Jobs memory${nc} ________________ ${red}${memory_per_job}${nc} Gb per job
${green}Network${nc} ____________________ ${red}${network}${nc}
${green}Working directory${nc} _________ '${ylo}${workdir}/${nc}'
${green}Fastq directory${nc} ___________ '${ylo}${fastq_dir}${nc}'
${green} > Fastq processed${nc} ________ ${red}${fastq_files}${nc} fastq files
${green} > Forward reads${nc} __________ ${red}${fastq_R1}${nc} R1
${green} > Reverse reads${nc} __________ ${red}${fastq_R2}${nc} R2
${blue}Modules:${nc}
${green} > Quality Control${nc} ________ ${red}${qualities}${nc}
${green} > Keep Trim${nc} ______________ ${red}${keeptrim}${nc}
${green} > Soft Clipping${nc} __________ ${red}${cleapping}${nc}
${green} > Cov Stats${nc} ______________ ${red}${covstats}${nc}
${green} > Consensus${nc} ______________ ${red}${consensus}${nc}
${green} > Lineages${nc} _______________ ${red}${lineages}${nc}
${green} > Gisaid${nc} _________________ ${red}${gisaid}${nc}
${blue}Params:${nc}
${green} > Reference genome${nc} _______ ${ylo}${reference}${nc}
${green} > Mapper${nc} ________________ ${ylo}${mapper}${nc}
${green} > Min coverage${nc} ___________ ${red}${min_cov}${nc} X
${green} > Min allele frequency${nc} ___ ${red}${min_freq}${nc}
${green} > Assigner${nc} _ ${red}${assigner}${nc}
${green} - Nextclade dataset${nc} _____ ${red}${nextclade_dataset}${nc}
${green} > Fastq-Screen subset${nc} ____ ${red}${fastqscreen_subset}${nc}
${green} > Cutadapt clipping${nc} ______ ${red}${cutadapt_clipping} nt${nc}
"
# Print settings message
echo -e "${message}"
# Log settings message
mkdir -p ${workdir}/results/10_Reports/ 2> /dev/null
echo -e "${message}" \
| sed "s/\x1B\[[0-9;]*[mK]//g" \
> ${workdir}/results/10_Reports/settings.log
mkdir -p ${workdir}/results/10_Reports/envs/ 2> /dev/null
cp ${workdir}/workflow/envs/*.yaml ${workdir}/results/10_Reports/envs/
cp ${config_file} ${workdir}/results/10_Reports/config.log 2> /dev/null
# If errors:
if [[ ! $(command -v conda) ]] # If no conda
then
return 0
elif [[ "${fastq}" == "0" ]] # If no FASTQ
then
echo -e "\n Cannot activate ${ylo}Workflow-Core${nc} conda environment."
return 0
fi
###############################################################################
### RUN SNAKEMAKE ###
#####################
# Print settings message
echo -e "
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Run Snakemake${nc} ${blue}#####${nc}
${blue}-------------------------${nc}
"
echo -e "
${green} > Snakemake: unlock working directory${nc}
"
echo -e "\n ${green} > Snakemake: unlock working directory${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
--rerun-incomplete \
--unlock
echo -e "
${green} > Snakemake: list conda environments${nc}
"
snakemake \
echo -e "\n ${green} > Snakemake: list conda environments${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
--list-conda-envs
echo -e "
${green} > Snakemake: create conda environments${nc}
"
echo -e "\n ${green} > Snakemake: create conda environments${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
--conda-create-envs-only \
--use-conda
echo -e "
${green} > Snakemake: dry run${nc}
"
echo -e "\n ${green} > Snakemake: dry run${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
......@@ -399,9 +192,7 @@ snakemake \
--dry-run \
--quiet host rules
echo -e "
${green} > Snakemake: run${nc}
"
echo -e "\n ${green} > Snakemake: run${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile\
......@@ -412,49 +203,12 @@ snakemake \
--use-conda \
--quiet host progress
# Deactive workflow-core conda environment.
echo -e "
Deactivate ${ylo}Workflow-Core${nc} conda environment."
conda deactivate
###############################################################################
### Gzip ###
############
# Gzip reports directory
#cd ${workdir}/results/
#tar -zcf 10_Reports_archive.tar.gz 10_Reports/
#cd ${workdir}
# Gzip results directory
#mkdir -p ${workdir}/archives/ 2> /dev/null
#tar -zcf archives/Results_${time_stamp_archive}_${reference}_${aligner}-${min_cov}X_${samples}sp_archive.tar.gz results/
###############################################################################
### Timer ###
#############
### DEACTIVATE WORKFLOW-CORE ###
#################################
# Timer
time_stamp_end=$(date +"%Y-%m-%d %H:%M") # Get date / hour ending analyzes
elapsed_time=${SECONDS} # Get SECONDS counter
hours=$((${elapsed_time}/3600)) # /3600 = hours
minutes=$(((${elapsed_time}%3600)/60)) # %3600 /60 = minutes
seconds=$((${elapsed_time}%60)) # %60 = seconds
formatted_time=$(printf "%02d:%02d:%02d" ${hours} ${minutes} ${seconds}) # Format
# Time message
message_time="
${green}Start time${nc} _____________ ${time_stamp_start}
${green}End time${nc} _______________ ${time_stamp_end}
${green}Processing time${nc} ________ ${ylo}${formatted_time}${nc}
"
# Print time message
echo -e "${message_time}"
# Log time message
echo -e "${message_time}" \
| sed "s/\x1B\[[0-9;]*[mK]//g" \
>> ${workdir}/results/10_Reports/settings.log
# Deactive workflow-core conda environment.
echo -e "\n Deactivate ${ylo}Workflow-Core${nc} conda environment."
conda deactivate
###############################################################################
###############################################################################
\ No newline at end of file
Snakemake: 0 → 100644
+ 0
− 0
View file @ 5d2f61d9
version.txt → VERSION_temp.txt
+ 0
− 0
View file @ 5d2f61d9
File moved
config/config.yaml
+ 8
− 7
View file @ 5d2f61d9
......@@ -25,13 +25,13 @@
fastq_dir: 'resources/reads/' # Path to reads fastq.gz files (default: 'resources/reads/') [PATH]
modules: # GeVarLi analysis modules, set 'true' or 'false' [BOOL]
qualities: true # Perform reads quality controls (FastQC, Fastq-Screen) (default: true)
keeptrim: false # Keep trimmed reads files (Cutadapt / Sickle-trim) (default: false)
clipping: false # Perform reads clipping (Bamclipper) (default: false)
covstats: true # Perform coverage statistics (Fagstat, Covstats) (default: true)
consensus: true # Perform reads mapping to reference (BWA, Minimap2, Bowtie2) (default: true)
lineages: true # Perform clade and lineage assignations (Nexclade, Pangolin) (default: true)
gisaid: false # Perform gisaid submission template (GisAid : TODO) (default: false)
qualities: true # Perform reads quality controls (FastQC, Fastq-Screen) (default: true)
keeptrim: false # Keep trimmed reads files (Cutadapt / Sickle-trim) (default: false)
clipping: false # Perform reads clipping (Bamclipper) (default: false)
covstats: true # Perform coverage statistics (Fagstat, Covstats) (default: true)
consensus: true # Perform reads mapping to reference (BWA, Minimap2, Bowtie2) (default: true)
lineages: true # Perform clade and lineage assignations (Nexclade, Pangolin) (default: true)
gisaid: false # Perform gisaid submission template (GisAid : TODO) (default: false)
consensus:
reference: 'SARS-CoV-2_Wuhan_MN908947.3' # Your reference, in fasta format (default: 'SARS-CoV-2_Wuhan_MN-908947-3') [STR]
......@@ -336,6 +336,7 @@ envs: # Conda environement yaml files:
sickle_trim: '../envs/sickle-trim_v.1.33.yaml' # Sickle-trim ver. 1.33
tsv2vcf: '../envs/tsv2vcf_v.2025.01.yaml' # tsv2vcf ver. 2025.01 (biopython=1.85 numpy=2.2.2 scipy=1.15.1)
workflow: '../envs/workflow-core.yaml' # workflow ver. 2025.01 (snakemake=8.27.1 graphviz=12.0.0)
yq: '../envs/yq_v.3.4.3.yaml' # yq ver. 3.4.3
report: # Snakemake reports formats
stat:
......
workflow/Snakefile
+ 11
− 7
View file @ 5d2f61d9
......@@ -28,6 +28,8 @@ configfile: "config/config.yaml"
#################
# Imports
import time, re
from snakemake.utils import min_version
from snakemake.utils import validate
......@@ -41,6 +43,7 @@ FASTQ_DIR = config["fastq_dir"]
VALID_FASTQ = get_valid_fastq(FASTQ_DIR)
SAMPLE = list(VALID_FASTQ.keys())
MATE = ["1", "2"]
START_TIME = time.time()
# Exports
import scripts.functions as functions
......@@ -60,7 +63,7 @@ functions.STAT_EXT = config["report"]["stat"]["extention"] # Stat reports extent
min_version("8.27.0")
# Schemas
#validate(config, schema="schemas/config.schema.yaml")
validate(config, schema="schemas/config.schema.yaml")
###############################################################################
### WILDCARDS ###
......@@ -81,9 +84,9 @@ TMP_DIR = config["resources"]["tmp_dir"] # Temporary directory
### ENVIRONMENTS ###
####################
MULTIQC = config["envs"]["multiqc"] # Multi-QC conda env
FASTQ_SCREEN = config["envs"]["fastq_screen"] # Fastq-Screen conda env
FASTQC= config["envs"]["fastqc"] # FastQC conda env
YQ = config["envs"]["yq"] # YQ conda environment
FASTQ_SCREEN = config["envs"]["fastq_screen"] # Fastq-Screen conda environment
FASTQC= config["envs"]["fastqc"] # FastQC conda environment
CUTADAPT = config["envs"]["cutadapt"] # Cutadapt conda environment
SICKLE_TRIM = config["envs"]["sickle_trim"] # Sickle-Trim conda environment
MINIMAP2 = config["envs"]["minimap2"] # BWA conda environment
......@@ -91,14 +94,15 @@ BWA = config["envs"]["bwa"] # BWA conda environment
BOWTIE2 = config["envs"]["bowtie2"] # Bowtie2 conda environment
SAMTOOLS = config["envs"]["samtools"] # SamTools conda environment
BEDTOOLS = config["envs"]["bedtools"] # BedTools conda environment
BAMCLIPPER = config["envs"]["bamclipper"] # BAMClipper
BAMCLIPPER = config["envs"]["bamclipper"] # BAMClipper onda environment
GAWK = config["envs"]["gawk"] # Awk (GNU) 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
NEXTCLADE = config["envs"]["nextclade"] # Nextclade conda environment
WORKFLOW = config["envs"]["workflow"] # Workflow conda environment
MULTIQC = config["envs"]["multiqc"] # Multi-QC conda environment
WORKFLOW = config["envs"]["workflow"] # Workflow conda environment
###############################################################################
### PARAMETERS ###
......@@ -196,6 +200,6 @@ include: "rules/workflow_reporting.smk"
rule all:
input:
report = "results/10_Reports/snakemake/workflow-report.html"
tarball = "results/Reports_archive.tar.gz"
###############################################################################
workflow/envs/workflow-core.yaml
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− 1
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......@@ -10,4 +10,4 @@ dependencies:
- snakemake-interface-report-plugins
- snakemake-interface-storage-plugins
- graphviz=12.0.0
- yq=3.4.3
- yq=3.4.3
\ No newline at end of file
workflow/envs/yq_v.3.4.3.yaml 0 → 100644
+ 7
− 0
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name: yq
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- yq=3.4.3
\ No newline at end of file
workflow/rules/symlinks_renamming.smk
+ 21
− 1
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......@@ -17,6 +17,25 @@
# Use ____________________ snakemake -s Snakefile --use-conda -j
###############################################################################
###############################################################################
rule config:
# Aim: Load configuration file
# Use: yq -r . <CONFIG_FILE>
message:
"""
~ Configuration ∞ Show analyses settings ~
"""
conda:
WORKFLOW
input:
config_file = "config/config.yaml"
output:
done = temp("done.temp")
shell:
"bash workflow/scripts/settings.sh "
"&& "
"touch {output.done}"
###############################################################################
rule symlinks:
# Aim: Create fastq files symlinks
......@@ -28,7 +47,8 @@ rule symlinks:
Reads: ___________ R{wildcards.mate}
"""
input:
valid_fastq = lambda wildcards: os.path.abspath(VALID_FASTQ[wildcards.sample][wildcards.mate])
valid_fastq = lambda wildcards: os.path.abspath(VALID_FASTQ[wildcards.sample][wildcards.mate]),
done = "done.temp"
output:
symlink = temp("results/symlinks/{sample}_R{mate}.fastq.gz")
log:
......
workflow/rules/workflow_reporting.smk
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− 16
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......@@ -17,6 +17,31 @@
# Use ____________________ snakemake -s Snakefile --use-conda -j
###############################################################################
###############################################################################
###############################################################################
rule tar_reports:
# Aim: compresses reports into a tarball
# Use: tar -zcf 10_Reports_archive.tar.gz 10_Reports/
message:
"""
~ Archive ∞ Compress reports ~
"""
input:
html_report = "results/10_Reports/workflow-report.html"
output:
tarball = "results/Reports_archive.tar.gz"
shell:
"tar " # Tar command
"-z " # Gzip compression
"-c " # Create a new archive
"-f " # Use archive file or device ARCHIVE
"{output.tarball} " # Output archive
"-C results/ " # Change to directory 'results/'
"10_Reports/" # Input directory to compress
###############################################################################
rule snakemake_report:
# Aim: generates a workflow report in HTML format
......@@ -30,20 +55,22 @@ rule snakemake_report:
params:
#style_sheet = STYLE_SHEET
input:
final_outputs = get_final_outputs(),
summary = "results/10_Reports/snakemake/files-summary.txt",
#graph = "results/10_Reports/snakemake/{graph_type}.{ext}",
multiqc = "results/10_Reports/multiqc/",
time = "results/10_Reports/time.log",
summary = "results/10_Reports/files-summary.txt",
graph = expand("results/10_Reports/graphs/{graph_type}.{ext}",
graph_type = GRAPH_TYPE,
ext = GRAPH_EXT),
output:
report = "results/10_Reports/snakemake/workflow-report.html"
html_report = "results/10_Reports/workflow-report.html"
log:
"results/10_Reports/tools-log/snakemake/workflow-report.log"
"results/10_Reports/tools-log/workflow-report.log"
shell:
"snakemake " # Snakemake
"--report " # Create an HTML report with results and statistics
"snakemake " # Snakemake
"--report " # Create an HTML report with results and statistics
#"--report-stylesheet {params.style_sheet} " # Custom stylesheet to use for report
" {output.report} " # Output report
"2> {log}" # Log redirection
" {output.html_report} " # Output report
"2> {log}" # Log redirection
###############################################################################
rule snakemake_summary:
......@@ -58,9 +85,9 @@ rule snakemake_summary:
input:
final_outputs = get_final_outputs()
output:
summary = "results/10_Reports/snakemake/files-summary.txt"
summary = "results/10_Reports/files-summary.txt"
log:
"results/10_Reports/tools-log/snakemake/files-summary.log"
"results/10_Reports/tools-log/files-summary.log"
shell:
"snakemake " # Snakemake
"--summary " # Print a summary of all files created by the workflow
......@@ -81,9 +108,9 @@ rule snakemake_graph:
input:
final_outputs = get_final_outputs()
output:
graph = "results/10_Reports/snakemake/{graph_type}.{ext}"
graph = "results/10_Reports/graphs/{graph_type}.{ext}"
log:
"results/10_Reports/tools-log/snakemake/{graph_type}-{ext}.log"
"results/10_Reports/tools-log/graphs/{graph_type}-{ext}.log"
shell:
"snakemake " # Snakemake
"--{wildcards.graph_type} " # Graph types: 'dag', 'rulegraph', 'filegraph'
......@@ -107,7 +134,9 @@ rule multiqc_aggregation:
input:
final_outputs = get_final_outputs()
output:
multiqc = directory("results/10_Reports/multiqc/")
multiqc = directory("results/10_Reports/multiqc/"),
html_report = "results/10_Reports/multiqc/multiqc_report.html",
copy_report = "results/All_QC_reports.html"
log:
"results/10_Reports/tools-log/multiqc.log"
shell:
......@@ -120,6 +149,100 @@ rule multiqc_aggregation:
"--export " # Export plots as static images in addition to the report
"--outdir {output.multiqc} " # -o: Create report in the specified output directory
"{input.final_outputs} " # Input final outputs
"> {log} 2>&1" # Log redirection
"> {log} 2>&1 " # Log redirection
"&& cp {output.html_report} {output.copy_report} " # Copy report to results directory
"2> /dev/null" # Suppress error messages
###############################################################################
rule log_time:
# Aim: log workflow start and end time
# Use: date +"%Y-%m-%d %H:%M"
message:
"""
~ Log ∞ Workflow time ~
"""
input:
final_outputs = get_final_outputs()
output:
time_log = "results/10_Reports/time.log"
run:
time_stamp_start = time.strftime("%Y-%m-%d %H:%M", time.localtime(start_time)) # Get system: analyzes starting time
time_stamp_end = time.strftime("%Y-%m-%d %H:%M", time.localtime()) # Get date / hour ending analyzes
elapsed_time = int(time.time() - start_time) # Get SECONDS counter
hours = elapsed_time // 3600 # /3600 = hours
minutes = (elapsed_time % 3600) // 60 # %3600 /60 = minutes
seconds = elapsed_time % 60 # %60 = seconds
formatted_time = f"{hours:02d}:{minutes:02d}:{seconds:02d}" # Format
green = "\033[32m" # ANSI green color code
ylo = "\033[33m" # ANSI yellow color code
nc = "\033[0m" # ANSI no-color code
message_time = f"""
{green}Start time{nc} _____________ {time_stamp_start}
{green}End time{nc} _______________ {time_stamp_end}
{green}Processing time{nc} ________ {ylo}{formatted_time}{nc}
"""
print(message_time) # Print time message
ansi_escape = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]') # ANSI escape code
message_clean = ansi_escape.sub('', message_time) # Clean ANSI escape code
with open(output.time_log, "w") as f: # Log time message
f.write(message_clean)
###############################################################################
rule log_setup:
# Aim: log user setup
# Use:
message:
"""
~ Log ∞ User setup ~
"""
input:
setup = "config/config.yaml",
output:
setup_log = "results/10_Reports/setup.log"
run:
import subprocess
uname = subprocess.check_output(["uname", "-a"]).decode().strip()
fastq_dir = subprocess.check_output(["yq", "-Mr", ".fastq_dir", input.setup]).decode().strip()
try:
fastq_files = subprocess.check_output(["bash", "-c", "ls -1 {}/*.fastq.gz 2>/dev/null | wc -l".format(fastq_dir)]).decode().strip()
except Exception:
fastq_files = "0"
with open(output.setup_log, "w") as f:
f.write("OS info: " + uname + "\n")
f.write("Fastq directory: " + fastq_dir + "\n")
f.write("Number of fastq files: " + fastq_files + "\n")
###############################################################################
rule log_environments:
# Aim: copy conda environments files to results
# Use: cp workflow/envs/*.yaml results/10_Reports/envs/
message:
"""
~ Log ∞ Workflow environments ~
"""
input:
envs = "workflow/envs"
output:
envs_log = directory("results/10_Reports/envs/")
shell:
"mkdir -p {output.envs_log} && " # Create directory
"cp {input.envs}/*.yaml {output.envs_log} " # Copy envs files
"2> /dev/null" # Suppress error messages
###############################################################################
\ No newline at end of file
###############################################################################
rule log_config:
# Aim: copy settings file to results
# Use: cp config/config.yaml results/10_Reports/config.log
message:
"""
~ Log ∞ Workflow configuration ~
"""
input:
config = "config/config.yaml"
output:
config_log = "results/10_Reports/config.log"
shell:
"cp {input.config} {output.config_log} " # Copy config file
"2> /dev/null" # Suppress error messages
###############################################################################
workflow/schemas/config.schema.yaml
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$schema: "http://json-schema.org/draft-07/schema#"
title: "GeVarLi Configuration Schema"
type: object
required:
- fastq_dir
- modules
- consensus
- gisaid
- nextclade
- ivar
- bamclipper
- bwa
- bowtie2
- minimap2
- sickle_trim
- cutadapt
- multiqc
- fastq_screen
- rename
- resources
- envs
- report
properties:
fastq_dir:
type: string
modules:
type: object
required:
- qualities
- keeptrim
- clipping
- covstats
- consensus
- lineages
- gisaid
properties:
qualities:
type: boolean
keeptrim:
type: boolean
clipping:
type: boolean
covstats:
type: boolean
consensus:
type: boolean
lineages:
type: boolean
gisaid:
type: boolean
consensus:
type: object
required:
- reference
- min_cov
- min_freq
- iupac
- mapper
- caller
- assigner
properties:
reference:
type: string
min_cov:
type: string
min_freq:
type: string
iupac:
type: string
mapper:
type: string
caller:
type: string
assigner:
type: string
gisaid:
type: object
required:
- username
- threshold
- name
- country
- identifier
- year
properties:
username:
type: string
threshold:
type: string
name:
type: string
country:
type: string
identifier:
type: string
year:
type: string
nextclade:
type: object
required:
- path
- dataset
properties:
path:
type: string
dataset:
type: string
ivar:
type: object
required:
- max_depth
- min_bq
- min_qual
- map_qual
properties:
max_depth:
type: string
min_bq:
type: string
min_qual:
type: string
map_qual:
type: string
bamclipper:
type: object
required:
- path
- primers
- upstream
- downstream
properties:
path:
type: string
primers:
type: string
upstream:
type: string
downstream:
type: string
bwa:
type: object
required:
- algorithm
properties:
algorithm:
type: string
bowtie2:
type: object
required:
- algorithm
- sensitivity
properties:
algorithm:
type: string
sensitivity:
type: string
minimap2:
type: object
required:
- preset
- algorithm
properties:
preset:
type: string
algorithm:
type: object
required:
- "k-mer_size"
- minimizer_size
- split_size
- homopolymer
properties:
"k-mer_size":
type: string
minimizer_size:
type: string
split_size:
type: string
homopolymer:
type: string
sickle_trim:
type: object
required:
- quality
- length
- command
- encoding
properties:
quality:
type: string
length:
type: string
command:
type: string
encoding:
type: string
cutadapt:
type: object
required:
- clipping
- length
- kits
properties:
clipping:
type: string
length:
type: string
kits:
type: object
required:
- truseq
- nextera
- small
properties:
truseq:
type: string
nextera:
type: string
small:
type: string
multiqc:
type: object
required:
- path
- config
- tag
properties:
path:
type: string
config:
type: string
tag:
type: string
fastq_screen:
type: object
required:
- config
- subset
- reference
properties:
config:
type: string
subset:
type: string
reference:
type: array
items:
type: string
rename:
type: object
required:
- barcode_id
- line_id
- end_id
properties:
barcode_id:
type: boolean
line_id:
type: boolean
end_id:
type: boolean
resources:
type: object
required:
- cpus
- ram
- tmp_dir
properties:
cpus:
type: string
ram:
type: string
tmp_dir:
type: string
envs:
type: object
required:
- bamclipper
- bcftools
- bedtools
- bowtie2
- bwa
- cutadapt
- fastq_screen
- fastqc
- gawk
- ivar
- minimap2
- multiqc
- nextclade
- pangolin
- samtools
- sickle_trim
- tsv2vcf
- workflow
properties:
bamclipper:
type: string
bcftools:
type: string
bedtools:
type: string
bowtie2:
type: string
bwa:
type: string
cutadapt:
type: string
fastq_screen:
type: string
fastqc:
type: string
gawk:
type: string
ivar:
type: string
minimap2:
type: string
multiqc:
type: string
nextclade:
type: string
pangolin:
type: string
samtools:
type: string
sickle_trim:
type: string
tsv2vcf:
type: string
workflow:
type: string
report:
type: object
required:
- stat
- graph
properties:
stat:
type: object
required:
- extention
properties:
extention:
type: array
items:
type: string
graph:
type: object
required:
- type
- extention
properties:
type:
type: array
items:
type: string
extention:
type: array
items:
type: string
\ No newline at end of file
workflow/scripts/__pycache__/functions.cpython-312.pyc
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workflow/scripts/functions.py
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......@@ -171,7 +171,11 @@ def get_final_outputs():
min_cov = MIN_COV,
caller = CALLER,
assigner = ASSIGNER))
# final_outpus
# logs
final_outputs.append("results/10_Reports/setup.log")
final_outputs.append("results/10_Reports/config.log")
final_outputs.append("results/10_Reports/envs/")
# return final_outpus
return final_outputs
###############################################################################
workflow/scripts/results/10_Reports/settings.log 0 → 100644
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workflow/scripts/settings.sh 0 → 100644
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#!/bin/bash
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
### ###
### /\ ______ ___ ____ _ _ __ ____ __ ____ ______ /\ ###
### || \ \ \ \ / __( ___( \/ )__\ ( _ ( ) (_ _) / / / / || ###
### || > > > > ( (_-.)__) \ /(__)\ ) /)(__ _)(_ < < < < || ###
### || /_/_/_/ \___(____) \(__)(__(_)\_(____(____) \_\_\_\ || ###
### \/ \/ ###
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ Run_GeVarLi.sh
# Version ________________ v.2025.03
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Bash script running GeVarLi snakefile
# Date ___________________ 2021.10.12
# Latest modifications ___ 2025.03.12
# Use ____________________ '. Run_GeVarLi.sh'
###############################################################################
###############################################################################
### ABOUT ###
#############
workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )"/../../ && pwd) # Get working directory
version=$(<${workdir}/VERSION_temp.txt) # Get version
blue="\033[1;34m" # blue
green="\033[1;32m" # green
red="\033[1;31m" # red
ylo="\033[1;33m" # yellow
nc="\033[0m" # no color
###############################################################################
### OPERATING SYSTEM ###
########################
shell=$SHELL # Get shell
# Get operating system
case "$OSTYPE" in
darwin*) os="osx" ;;
linux*) os="linux" ;;
bsd*) os="bsd" ;;
solaris*) os="solaris" ;;
msys*) os="windows" ;;
cygwin*) os="windows" ;;
*) os="unknown (${OSTYPE})" ;;
esac
###############################################################################
### HARDWARE ###
################
if [[ ${os} == "osx" ]]
then
model_name=$(sysctl -n machdep.cpu.brand_string) # Get chip model name
physical_cpu=$(sysctl -n hw.physicalcpu) # Get physical cpu
logical_cpu=$(sysctl -n hw.logicalcpu) # Get logical cpu
mem_size=$(sysctl -n hw.memsize) # Get memory size (bit)
ram_gb=$(expr ${mem_size} \/ $((1024**3))) # mem_size / 1024**3 = Gb
elif [[ ${os} == "linux" || ${os} == "bsd" || ${os} == "solaris" ]]
then
model_name=$(lscpu | grep -o -E "Model name: +.+" | sed -E "s/Model name: +//") # Get chip model name
physical_cpu=$(lscpu | grep -o -E "^CPU\(s\): +[0-9]+" | sed -E "s/CPU\(s\): +//") # Get physical cpu
threads_cpu=$(lscpu | grep -o -E "^Thread\(s\) per core: +[0-9]+" | sed -E "s/Thread\(s\) per core: +//") # Get thread(s) per core
logical_cpu=$(expr ${physical_cpu} \* ${threads_cpu}) # Calcul logical cpu
mem_size=$(grep -o -E "MemTotal: +[0-9]+" /proc/meminfo | sed -E "s/MemTotal: +//") # Get memory size (Kb)
ram_gb=$(expr ${mem_size} \/ $((1024**2))) # mem_size / 1024**2 = Gb
else
echo -e "\n Please, use an '${ylo}UNIX${nc}' operating system, like:
> '${green}linux${nc}'
> '${green}osx${nc}'
> '${green}WSL${nc}' \n"
return 0
fi
###############################################################################
### NETWORK ###
###############
if ping -c 1 -W 5 google.com > /dev/null 2>&1 || \
ping -c 1 -W 5 cloudflare.com > /dev/null 2>&1
then
network="Online"
else
network="Offline"
fi
###############################################################################
### CONDA ###
#############
message_conda="
$(conda --version)
Path: $(which conda)
$(conda config --show channels)
"
###############################################################################
### CONFIGURATION ###
#####################
conda_version=$(conda --version | sed 's/conda //') # Conda version
mamba_version=$(mamba --version | head -n 1 | sed 's/mamba //') # Mamba version
snakemake_version=$(snakemake --version) # Snakemake version
fastq_dir=$(yq -Mr '.fastq_dir' ${config_file}) # Get path to fastq files directory
fastq_files=$(/bin/ls -l ${fastq_dir}/*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get fastq.gz files count
fastq_R1=$(/bin/ls -l ${fastq_dir}/*R1*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R1 fastq files count
fastq_R2=$(/bin/ls -l ${fastq_dir}/*R2*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R2 fastq files count
max_threads=$(yq -Mr '.resources.cpus' ${config_file}) # Get user config: max threads
max_memory=$(yq -Mr '.resources.ram' ${config_file}) # Get user config: max memory (Gb)
qualities=$(yq -Mr '.modules.qualities' ${config_file}) # Reads QC
keeptrim=$(yq -Mr '.modules.keeptrim' ${config_file}) # Keep trimmed reads
cleapping=$(yq -Mr '.modules.cleapping' ${config_file}) # Reads cleapping
covstats=$(yq -Mr '.modules.covstats' ${config_file}) # Mapping coverage stats
consensus=$(yq -Mr '.modules.consensus' ${config_file}) # Consensus
lineages=$(yq -Mr '.modules.lineages' ${config_file}) # Lineages assignation
gisaid=$(yq -Mr '.modules.gisaid' ${config_file}) # Gisaid submission file
# Get user config: genome reference
reference=$(yq -Mc '.consensus.reference' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: mapper
mapper=$(yq -Mc '.consensus.mapper' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: minimum coverage
min_cov=$(yq -Mc '.consensus.min_cov' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: minimum allele frequency
min_freq=$(yq -Mr '.consensus.min_freq' ${config_file})
# Get user config: assigner tool
assigner=$(yq -Mc '.consensus.assigner' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
# Get user config: hard clipping option
hard_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
# Get user config: dataset for nextclade
nextclade_dataset=$(yq -Mc '.nextclade.dataset' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//')
# Get user config: fastq_screen subsetption
fastqscreen_subset=$(yq -Mr '.fastq_screen.subset' ${config_file})
# Get user config: cutadapt clipping
cutadapt_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
message_settings="""
${blue}------------------------------------------------------------------------${nc}
${blue}#####${nc} ${red}Configuration${nc} ${blue}#####${nc}
${blue}-------------------------${nc}
${green}Starting time${nc} ______________ ${time_stamp_start}
${green}Conda version${nc} ______________ ${ylo}${conda_version}${nc}
${green}Mamba version${nc} ______________ ${ylo}${mamba_version}${nc}
${green}Snakemake version${nc} __________ ${ylo}${snakemake_version}${nc}
${green}Max threads${nc} ________________ ${red}${max_threads}${nc} of ${ylo}${logical_cpu}${nc} threads available
${green}Max memory${nc} _________________ ${red}${max_memory}${nc} of ${ylo}${ram_gb}${nc} Gb available
${green}Jobs memory${nc} ________________ ${red}${memory_per_job}${nc} Gb per job
${green}Network${nc} ____________________ ${red}${network}${nc}
${green}Working directory${nc} _________ '${ylo}${workdir}/${nc}'
${green}Fastq directory${nc} ___________ '${ylo}${fastq_dir}${nc}'
${green} > Fastq processed${nc} ________ ${red}${fastq_files}${nc} fastq files
${green} > Forward reads${nc} __________ ${red}${fastq_R1}${nc} R1
${green} > Reverse reads${nc} __________ ${red}${fastq_R2}${nc} R2
${blue}Modules:${nc}
${green} > Quality Control${nc} ________ ${red}${qualities}${nc}
${green} > Keep Trim${nc} ______________ ${red}${keeptrim}${nc}
${green} > Soft Clipping${nc} __________ ${red}${cleapping}${nc}
${green} > Cov Stats${nc} ______________ ${red}${covstats}${nc}
${green} > Consensus${nc} ______________ ${red}${consensus}${nc}
${green} > Lineages${nc} _______________ ${red}${lineages}${nc}
${green} > Gisaid${nc} _________________ ${red}${gisaid}${nc}
${blue}Params:${nc}
${green} > Reference genome${nc} _______ ${ylo}${reference}${nc}
${green} > Mapper${nc} ________________ ${ylo}${mapper}${nc}
${green} > Min coverage${nc} ___________ ${red}${min_cov}${nc} X
${green} > Min allele frequency${nc} ___ ${red}${min_freq}${nc}
${green} > Assigner${nc} _ ${red}${assigner}${nc}
${green} - Nextclade dataset${nc} _____ ${red}${nextclade_dataset}${nc}
${green} > Fastq-Screen subset${nc} ____ ${red}${fastqscreen_subset}${nc}
${green} > Cutadapt clipping${nc} ______ ${red}${cutadapt_clipping} nt${nc}
"""
# Print settings message
echo -e "${message}"
# Log settings message
mkdir -p ${workdir}/results/10_Reports/ 2> /dev/null
echo -e "${message}" \
| sed "s/\x1B\[[0-9;]*[mK]//g" \
> ${workdir}/results/10_Reports/settings.log
\ No newline at end of file
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