Instructions and script for setting up any nf-core pipeline on an offline system that has docker but not singularity available

[vmkalbskopf]

If you are in my position, where you need to run an nf-core pipeline on a system with docker but not singularity, you will find yourself a little stuck.
The nf-core tool will download singularity images for you, but not docker.
Here is how to set things up for a pure docker profile run of nextflow nf-core.

Follow these instructions to start with. Then instead of running the nf-core download tool (Pipeline code heading), run this script:

#!/usr/bin/env python3
import json
import subprocess
import argparse
import os

####################### Usage #############################
# ./download_nf-core_docker_images.py nf-core/pipeline_name
# example:
# ./download_nf-core_docker_images.py nf-core/rnaseq
###########################################################


parser = argparse.ArgumentParser()
parser.add_argument("nf_core")
args = parser.parse_args()

core_module = args.nf_core
module = core_module.replace('/', '_')


# find which docker images are used in the pipeline you specified, 
# and save it as a json file
if os.path.isfile(f'{module}_image_list.json')== False:
    with open(f'{module}_image_list.json', "w") as j_out:
        subprocess.run(["nextflow","inspect", core_module, "-profile", "test,docker", "--outdir", "testing"], stdout=j_out)

# load json as a list of dicts of images
with open(f'{module}_image_list.json', "r") as j_in:
    j = json.load(j_in)
    conts = j['processes']

# create folder for images if it doesn't exist
if os.path.exists(f'{module}_images') == False:
    os.mkdir(f'{module}_images')

# save each image in the folder
for d in conts:
    image = d["container"]
    name = image.split('/')[-1].replace(":", "_")
    subprocess.run([
         "docker", "save",
         image, "--output", 
         f"{module}_images/{name}.tar"])
    print(f"saved image: {image} to \t {module}_images/{name}.tar ")

Transfer the directory with the tar image files to the offline system.
Then run this inside the directory with the tar files to load them into your docker environment so nextflow can access them:
ls -1 *.tar | xargs --no-run-if-empty -L 1 docker load -i

And you're all set!
Let me know if I'm missing something.