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

Fix MEGAHIT process on resume #516

Merged
merged 4 commits into from
Sep 27, 2023
Merged

Fix MEGAHIT process on resume #516

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
e4860c4
Update megahit.nf
prototaxites Sep 27, 2023
f994012
Update CHANGELOG.md
prototaxites Sep 27, 2023
4a8ca9a
Merge branch 'dev' into fix_megahit
prototaxites Sep 27, 2023
6ce28af
Merge branch 'dev' into fix_megahit
jfy133 Sep 27, 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
7 changes: 4 additions & 3 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- [#511](https://github.com/nf-core/mag/pull/511) Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
- [#511](https://github.com/nf-core/mag/pull/511) - Update to nf-core 2.10 `TEMPLATE` (by @jfy133)

### `Fixed`

- [#515](https://github.com/nf-core/mag/pull/515) Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
- [#514](https://github.com/nf-core/mag/pull/514) Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
- [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
- [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
- [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)

### `Dependencies`

Expand Down
5 changes: 5 additions & 0 deletions modules/local/megahit.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,11 @@ process MEGAHIT {
mem = task.memory.toBytes()
if ( !params.megahit_fix_cpu_1 || task.cpus == 1 )
"""
## Check if we're in the same work directory as a previous failed MEGAHIT run
if [[ -d MEGAHIT ]]; then
rm -r MEGAHIT/
fi

megahit $args -t "${task.cpus}" -m $mem $input -o MEGAHIT --out-prefix "MEGAHIT-${meta.id}"

gzip -c "MEGAHIT/MEGAHIT-${meta.id}.contigs.fa" > "MEGAHIT/MEGAHIT-${meta.id}.contigs.fa.gz"
Expand Down
Loading