BrunoGrandePhD

#!/bin/bash

#
# This script uploads your public SSH key ('id_ed25519' by default)
# to the home directories of 'ec2-user' and 'ssm-user'. While both
# users are configured, it's recommended to use 'ec2-user' for SSH.
# Written by Bruno Grande.
#
# Script usage:
#

BrunoGrandePhD

name: docker-ci

on:
  push:
    branches: [main]
    tags: ['v[0-9]*', '[0-9]+.[0-9]+*']  # Match tags that resemble a version
  workflow_dispatch:  # Allow manually triggering the workflow

jobs:
  docker-build:

BrunoGrandePhD

patient,gender,status,sample,lane,fastq_1,fastq_2
S000,XX,0,S000-1234N,S000-1234N_M1,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
S001,XX,0,S001-1234N,S001-1234N_M2,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
S002,XX,0,S002-1234N,S002-1234N_M4,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
S003,XX,0,S003-1234N,S003-1234N_M5,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/n

BrunoGrandePhD

BrunoGrandePhD

BrunoGrandePhD

Instructions

These instructions are intended for Linux.

1. Install Miniconda 3.
2. Create conda environment using the attached environment.yml file:

   conda env create -n vep -f environment.yml

3. Download VEP cache and decompress the TAR archive:

BrunoGrandePhD

# Set up Synapse client and JSON Schema service
import synapseclient
syn = synapseclient.login()
syn.get_available_services()  # Output: ['json_schema']
js = syn.service("json_schema")

# Create, manage, and delete a JSON Schema organization
my_org = js.JsonSchemaOrganization("bgrande.test.new")
my_org  # Output: JsonSchemaOrganization(name='bgrande.test.new')
my_org.create()

BrunoGrandePhD

BrunoGrandePhD

library(ggplot2)

data <- data.frame(x = rnorm(1000, 1))

ggplot(data, aes(x)) + 
  geom_histogram(binwidth = 0.3, boundary = 0) + 
  geom_vline(xintercept = 0)

BrunoGrandePhD

library(ggplot2)
library(cowplot)  # For better ggplot2 theme
library(ggbeeswarm)  # For geom_quasirandom()

set.seed(1)

data <- data.frame(value = c(rnorm(100, -1.8), rnorm(100, 1.8)))

extra <- list(scale_x_discrete(labels = NULL, name = NULL),
              scale_y_continuous(name = NULL))