Skip to content

Commit

Permalink
fix(input_resources.smk): disable container
Browse files Browse the repository at this point in the history
Disables the singularity container for unzipping the Bcl2Fastq results.

The mambaforge container does not have zip as a command,
and busybox - which does - requires authentication to pull,
making it incompatible for use on a HPC.
  • Loading branch information
rbpatt2019 committed Dec 7, 2021
1 parent 89592ff commit c8612fb
Showing 1 changed file with 3 additions and 0 deletions.
3 changes: 3 additions & 0 deletions workflow/rules/input_resources.smk
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
# To guarantee they meet certain formats, naming conventions, etc.


# Disable container
# Mambaforge doesn't have zip, and busybox requires authentication to pull
rule unpack_bcl2fastq:
input:
**get_bcl_results(),
Expand All @@ -12,6 +14,7 @@ rule unpack_bcl2fastq:
"results/logs/unpack_bcl2fastq/unpack_bcl2fastq.log",
benchmark:
"results/benchmarks/unpack_bcl2fastq/unpack_bcl2fastq.txt"
container: None
shell:
"unzip "
"{input.bcl_zip} "
Expand Down

0 comments on commit c8612fb

Please sign in to comment.