Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update MEGAHIT container URLs #3689

Closed
wants to merge 4 commits into from
Closed

Update MEGAHIT container URLs #3689

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
9f61438
Update MEGAHIT container URLs
gariem Aug 1, 2023
0b80d1e
Using gzip until Docker image gets updated
gariem Aug 1, 2023
f003191
Merge branch 'master' into patch-2
adamrtalbot Aug 2, 2023
ec365b0
Update modules/nf-core/megahit/main.nf
gariem Aug 2, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 4 additions & 10 deletions modules/nf-core/megahit/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process MEGAHIT {

conda "bioconda::megahit=1.2.9 conda-forge::pigz=2.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' :
'biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }"
'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2' :
'biocontainers/megahit:1.2.9--h5b5514e_3' }"

input:
tuple val(meta), path(reads)
Expand Down Expand Up @@ -33,10 +33,7 @@ process MEGAHIT {
$args \\
--out-prefix $prefix

pigz \\
--no-name \\
-p $task.cpus \\
$args2 \\
gzip \\
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Was pigz included for a reason? I'd like to check before discarding.

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Pigz runs the compression taks faster (in parallel), but sadly it's not included in the docker image provided by the author. I have requested it to be added as well here: voutcn/megahit#360

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
Loading