https://github.com/nanoporetech/dorado
dorado: https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.3-linux-x64.tar.gzhttps://dropoff.nbi.ac.uk/pickup?claimID=HejmBN7XJVbMRv74&claimPasscode=mxpYSGxyhKCmJG5z&emailAddr=1017
Claim ID: HejmBN7XJVbMRv74
| #!/usr/bin/env python | |
| import argparse | |
| import sys | |
| import os | |
| import pandas as pd | |
| from biom import load_table, Table | |
| def merge_biom_files_with_pandas(biom_files): | |
| dfs = [] # List to store DataFrames |
| --[[ | |
| SLURM job submit filter for QOS | |
| Some code and ideas pulled from https://github.com/edf-hpc/slurm-llnl-misc-plugins/blob/master/job_submit.lua | |
| --]] | |
| --########################################################################-- | |
| -- |
| import os | |
| import csv | |
| import argparse | |
| def scan_paired_end_files(dir_path, pattern_list): | |
| # Initialize a list to store the sample IDs and file paths | |
| samples = [] | |
| # Loop through all files in the directory | |
| for file_name in os.listdir(dir_path): |
| library(patchwork) | |
| library(ggplot2) | |
| library(tidyverse) | |
| data(mtcars) | |
| data(iris) | |
| mtcars.tf <- mtcars %>% | |
| rownames_to_column("name") %>% | |
| pivot_longer(names_to = "metrics", values_to = "values", mpg:carb) |
| - hosts: all | |
| become: true | |
| become_user: root | |
| vars: | |
| singularity_version: 3.10.0 | |
| pre_tasks: | |
| - name: Update apt packages | |
| apt: | |
| update_cache: true | |
| cache_valid_time: 86400 #One day |
| #!/usr/bin/env python | |
| import requests | |
| import time | |
| import pathlib | |
| from joblib import Parallel, delayed | |
| from pqdm.processes import pqdm | |
| def url_template(id): | |
| url0 = "https://pubmlst.org/bigsdb?db=pubmlst_campylobacter_isolates&page=plugin&name=Contigs&format=text&isolate_id=" | |
| url1 = "&match=1&pc_untagged=0&min_length=&header=1" |
| library(dplyr) | |
| library(ggtree) | |
| tree <- read.tree("Benchmarking_tree_07Dec21.nwk") | |
| tips <- tree$tip.label %>% | |
| tibble(tip = .) %>% | |
| mutate(sample = gsub("_[a-zA-Z\\_]+","",tip)) | |
| #!/usr/bin/env nextflow | |
| nextflow.enable.dsl=2 | |
| ch_pilon = Channel.fromPath(params.sample_sheet) | |
| .splitCsv(header: true) | |
| .map {row -> tuple(row.sample_id,[row.sr1,row.sr2],row.contigs)} | |
| ch_pilon.view() |
| library(tidyverse) | |
| library(data.table) | |
| library(janitor) | |
| csv <- fread("Ebenn_code_data_21Jul21_18.08.csv") | |
| features <- names(csv)[-c(1,2,4)] | |
| sample_names <- csv$Name %>% | |
| gsub("_flye_[a-z\\_]*|_hybrid","",.) %>% |