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molikd / otb

Only The Best (Genome Assembly Tools)
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IMG files showing up in home folder, can those go in folder assembly run? maybe need some config #3

Closed scottgeib closed 3 years ago

scottgeib commented 3 years ago

(base) [scott.geib@ceres ~]$ pwd /home/scott.geib

-rwxrwxr-x. 1 scott.geib scott.geib 438M Sep 8 20:07 dmolik-blobtools.img -rwxrwxr-x. 1 scott.geib scott.geib 521M Sep 8 19:52 dmolik-genomescope2.img -rwxrwxr-x. 1 scott.geib scott.geib 74M Sep 8 19:53 dmolik-hifiasm.img -rwxrwxr-x. 1 scott.geib scott.geib 59M Sep 8 19:53 dmolik-jellyfish.img -rwxrwxr-x. 1 scott.geib scott.geib 400M Sep 8 19:56 dmolik-pbadapterfilt.img -rwxrwxr-x. 1 scott.geib scott.geib 392M Sep 8 19:58 dmolik-ragtag.img -rwxrwxr-x. 1 scott.geib scott.geib 122M Sep 8 20:00 dmolik-shhquis.img

molikd commented 3 years ago

They should be defaulting to ./work/singuarlity

This problem is from prefetch_containers.sh where without direction prefetch would place images in a deault direction. not prefetch defaults to the NXF_SINGULARITY_CACHEDIR if it exists, or to the first argument of the script.

utilizing the new otb.nf fixes the problem.

This problem has been fixed in an earlier commit, but is defintely fixed in e9d7515