Useful nextflow bash functions

nextflow-bash.sh

# Shortcut for going to work directories
# Usage: gw <workdir pattern>
# Replace the work directory below as needed
# Where workdir pattern is something like "ab/afedeu"
function gw {
    path=`ls --color=none -d /path/to/work/directory/$1*`
    cd $path
}

# Go work that fetches work dir from .nextflow.log
function gw {
  workdir=$(cat "`git rev-parse --show-toplevel`/.nextflow.log" | grep 'Work-dir:' | grep -Eo '/.[^ ]+ | grep -v "/ext"' | tr -d ' ')
  cd ${workdir}/$1*
}

function cd3 {
    cd $(git rev-parse --show-toplevel)
}

# sq squeue alternative
# Outputs more complete information about jobs including the work directory
function sq() {
    squeue --user `whoami` --format='%.18i %50j %10u %.10C %m %20J %M %.2t %n %R %Z' | awk -v OFS='\t' '{ match($10, /([a-f0-9]{2}\/[a-f0-9]{6})/, arr); print $1, $2, $3, $4, $5, $6, $7, $8, $9, arr[1] }' 
}

function ttt {
    cd `git rev-parse --show-toplevel`
}