thanhleviet

#!/usr/bin/env nextflow
nextflow.enable.dsl=2
ch_pilon = Channel.fromPath(params.sample_sheet)
                    .splitCsv(header: true)
                    .map {row -> tuple(row.sample_id,[row.sr1,row.sr2],row.contigs)}

ch_pilon.view()

thanhleviet

library(tidyverse)
library(data.table)
library(janitor)

csv <- fread("Ebenn_code_data_21Jul21_18.08.csv")

features <- names(csv)[-c(1,2,4)]

sample_names <- csv$Name %>% 
  gsub("_flye_[a-z\\_]*|_hybrid","",.) %>% 

thanhleviet

#Generate barcode indexes for NBD96 kit
rm(list = ls())
library(dplyr)
library(data.table)

index <- sapply(seq(1:6), function(x) paste0(LETTERS[1:8],x)) %>% t() %>% as.vector()

bc <- list()

letter_length <- 8

thanhleviet

#!/usr/bin/env python3
"""
Running this script is (intended to be) equivalent to running the following Snakefile:

include: "pipeline.conf"  # Should be an empty file

shell.prefix("set -euo pipefail;")

rule all:
    input:

thanhleviet

Bootstrap: docker
From: ubuntu:xenial


%labels
    Author: Thanh Le Viet
    Software: pangolin
    Description: "Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages"
    Notes: "This singularity definition is based on https://github.com/StaPH-B/docker-builds"

thanhleviet

libvirt + prometheus + grafana

KVM を libvirt でホストしていて、prometheus と grafana で観測したい場合。 exporter の実装は 3 種類みつかる。流儀が異なり、メトリクスが異なるので注意。

• libvirt_exporter (Go)
  • grafana json + prometheus recording rule
  • prometheus の設定ファイルで recording rule を有効化します。
  • job 名は libvirt_exporter

thanhleviet

# List of cheatsheet for linux find.
# Taken from here http://alvinalexander.com/unix/edu/examples/find.shtml

# basic 'find file' commands
# --------------------------
find / -name foo.txt -type f -print             # full command
find / -name foo.txt -type f                    # -print isn't necessary
find / -name foo.txt                            # don't have to specify "type==file"
find . -name foo.txt                            # search under the current dir
find . -name "foo.*"                            # wildcard

thanhleviet

#Required libraries
library(tidyverse)
library(rgdal)
library(rgeos)
library(broom)
library(maps)
#Postcode spatial data
#You need postcode map here https://www.opendoorlogistics.com/wp-content/uploads/Data/UK-postcode-boundaries-Jan-2015.zip
england <- readOGR( 
  dsn= "./osm/postcode/Distribution/" , 

thanhleviet

#!/usr/bin/env bash
# Author: Thanh Le Viet
# This script will split every consecutive fast5 files into a batch file list  for basecalling with guppy
# It is used for "live" basecalling while the sequencing still running on another machine.
# Command: bash ./run_basecalling.sh
# summary_file="sequencing_summary_FAO15487_23198198.txt"
# Usage: run watch_and_basecalling.sh sequencing_summary_FAO15487_23198198.txt
# Note: each run has a different summary_file name.

summary_file=$1

thanhleviet

params.reads = "/beegfs/sars-cov2/Test_060420"

ch_reads = Channel.fromFilePairs(params.reads + "/" + "*_R{1,2}_001.fastq.gz", flat: true)

ch_reads
        .map {
            it -> [it[0].replaceAll(~/\_L00[1,2,3,4]/,""), it[1], it[2]]
        }
        .groupTuple(by:0)
        .into {ch_reads_in; ch_test}