joelnitta

#!/usr/bin/bash

# Kill the job using the saved ID
kill -9 `cat dockerd.pid`
rm dockerd.pid
rm dockerd.log

joelnitta

#!/usr/bin/bash

# Start docker daemon in background
nohup dockerd-rootless.sh --experimental --storage-driver vfs >| dockerd.log 2>&1 &
# Save the process ID so we can kill it later
echo $! > dockerd.pid

joelnitta

in1:
  class: File
  path: raw-sequence.fastq.gz
out1: trimmed.fastq.gz 
html: report.html
json: report.json

joelnitta

cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/fastp:0.20.1--h8b12597_0

baseCommand: fastp

inputs:

joelnitta

---
title: "Resume"
output:
  rmarkdown::word_document:
    reference_docx: "custom-reference-2.docx"
---

##### Employer: Apple   Date: 2000

joelnitta

#!/usr/bin/bash

# Kill the job using the saved ID
kill -9 `cat dockerd.pid`
rm dockerd.pid
rm dockerd.log

joelnitta

#!/usr/bin/bash

# Start docker daemon in background
nohup dockerd-rootless.sh --experimental --storage-driver vfs >| dockerd.log 2>&1 &
# Save the process ID so we can kill it later
echo $! > dockerd.pid

joelnitta

# Set working directory
setwd(here::here())

# Load packages and functions
source("r-code/01_start_up.R")

# Load plan
source("r-code/plan.R")

# Load cache

joelnitta

joelnitta@Joels-iMac repos % git clone https://github.com/joelnitta/i18n
Cloning into 'i18n'...
remote: Enumerating objects: 1672, done.
remote: Total 1672 (delta 0), reused 0 (delta 0), pack-reused 1672
Receiving objects: 100% (1672/1672), 2.73 MiB | 2.43 MiB/s, done.
Resolving deltas: 100% (1167/1167), done.
joelnitta@Joels-iMac repos % cd i18n
joelnitta@Joels-iMac i18n % git submodule init
Submodule 'git-novice' (https://github.com/swcarpentry-i18n/git-novice.git) registered for path 'git-novice'
Submodule 'po4gitbook' (https://github.com/swcarpentry-i18n/po4gitbook.git) registered for path 'po4gitbook'

joelnitta

#' Write out a list of DNA sequences in chunks
#' 
#' The list will be split into a list of lists, to
#' save memory when writing out sequences.
#'
#' @param fasta_list The list of DNA sequences
#' @param chunk_size Size of chunks to split up list into.
#' @param out_dir Directory to write to
#'
#' @return List of hashes; digest of each chunk. Externally, the