Skip to content

Commit

Permalink
Using gzip until Docker image gets updated
Browse files Browse the repository at this point in the history
As per voutcn/megahit#360 pigz is not currently installed in the MEGAHIT biocontainer images (singularity: https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2 - docker: quay.io/biocontainers/megahit:1.2.9--h5b5514e_3). Therefore, the NF-Core module will fail to compress the contigs using pigz. 

This commit resolves the described fix.
  • Loading branch information
gariem authored Aug 1, 2023
1 parent 9f61438 commit 0b80d1e
Showing 1 changed file with 2 additions and 8 deletions.
10 changes: 2 additions & 8 deletions modules/nf-core/megahit/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,7 @@ process MEGAHIT {
$args \\
--out-prefix $prefix
pigz \\
--no-name \\
-p $task.cpus \\
$args2 \\
gzip \\
megahit_out/*.fa \\
megahit_out/intermediate_contigs/*.fa
Expand All @@ -54,10 +51,7 @@ process MEGAHIT {
$args \\
--out-prefix $prefix
pigz \\
--no-name \\
-p $task.cpus \\
$args2 \\
gzip \\
megahit_out/*.fa \\
megahit_out/intermediate_contigs/*.fa
Expand Down

0 comments on commit 0b80d1e

Please sign in to comment.