pditommaso

{ cat <<EOF
aws s3 ls s3://bucket/prefix1
aws s3 ls s3://bucket/prefix2
aws s3 ls s3://bucket/prefix3
EOF
} | xargs -I{} -P 10 bash -c "{}"

pditommaso

params.filter_seqs = 'NO_FILTER'
filter_file = file(params.filter_seqs)

process foo {
  input:
  file filter_file 

  script:
  def filter_argument = filter_file.name != 'NO_FILTER' ? "--filter ${params.filter_seqs}" : ''

pditommaso

params.filter_seqs = 'NO_FILTER'
filter_file = file(params.filter_seqs)

process foo {
  input:
  file filter_file 

  script:
  def filter_argument = filter_file.name != 'NO_FILTER' ? "--filter ${params.filter_seqs}" : ''

pditommaso

#
# generate 01compositional.bed.gz
#

# low-complexity by mDUST
mdust hs37d5.fa -c -w7 -v28 \
  | hs37d5.mdust-w7-v28.txt \
  | cut -f1,3,4 \
  | gawk -vOFS="\t" '{--$2;print}' \
  | bgzip > 01compositional/hs37d5.mdust-w7-v28.bed.gz

pditommaso

public class Generics {

    void wildcard() {
        List<?> stuff = new ArrayList<>();
        stuff.add("xx");            // NOT ok
        stuff.add(new Object());    // NOT ok
        stuff.size();               // OK

        List<?> a = new ArrayList<Object>();    // OK
        List<?> b = new ArrayList<String>();    // OK

pditommaso

#!/bin/bash
#
# this script will attempt to detect any ephemeral drives on an EC2 node and create a RAID-0 stripe
# mounted at /mnt. It should be run early on the first boot of the system.
#
# Beware, This script is NOT fully idempotent.
#
METADATA_URL_BASE="http://169.254.169.254/2012-01-12"

yum -y -d0 install mdadm curl

pditommaso

import java.nio.channels.FileLock

final file = new RandomAccessFile(new File("foo.lock"), "rw")
println "<Entering in critical section>"
try {
    /* 
     * wait to acquire a lock 
     */
    def secs = 0
    FileLock lock

pditommaso

Save NextFlow logo as this file.

pditommaso

// define a grammar called Hello
grammar Hello;
r   : 'hello' ID;
ID  : [a-z]+ ;
WS  : [ \t\r\n]+ -> skip ;

pditommaso

spinner()
{
    local pid=$1
    local delay=0.75
    local spinstr='|/-\'
    while [ "$(ps a | awk '{print $1}' | grep $pid)" ]; do
        local temp=${spinstr#?}
        printf " [%c]  " "$spinstr"
        local spinstr=$temp${spinstr%"$temp"}
        sleep $delay