Climb

[WhalleyT]

Made some changes to run the pipeline on CLIMB Jupyterhub. The changes in short are:

• Allocate resources expliciltly in every process (60ad35f).
• change permissions of files in bin to be copied into docker (42f28b8)
• add bin to docker (97276e9)
• change parse of some of the paths in case they are in S3 (45e6628)
• break up processes which contain jq into two so that jq output can be passed into a path variable to deal with S3 (b93a189)
• profile in nextflow.config

I've ran it again locally but will test a few more times to confirm.