diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ffd9c45..c8bc3b12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,15 +7,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#408] Added preprint citation information to README and manifest (added by @jfy133) +- [#408](https://github.com/nf-core/taxprofiler/pull/408) Added preprint citation information to README and manifest (added by @jfy133) ### `Fixed` -- [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#406] Fixed overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#405](https://github.com/nf-core/taxprofiler/pull/405) Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#406](https://github.com/nf-core/taxprofiler/pull/406) Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#409](https://github.com/nf-core/taxprofiler/pull/409) Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` +| Tool | Previous version | New version | +| -------------- | ---------------- | ----------- | +| megan/rma2info | 6.21.7 | 6.24.20 | + ### `Deprecated` ## v1.1.1 - Augmented Akita Patch [2023-10-11] diff --git a/modules.json b/modules.json index 9dc77080..aa63d31d 100644 --- a/modules.json +++ b/modules.json @@ -163,7 +163,7 @@ }, "megan/rma2info": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "dbce8951ff9a39ad08d87e563636bbcc6ef34032", "installed_by": ["modules"] }, "metaphlan/mergemetaphlantables": { diff --git a/modules/nf-core/megan/rma2info/environment.yml b/modules/nf-core/megan/rma2info/environment.yml new file mode 100644 index 00000000..471e5507 --- /dev/null +++ b/modules/nf-core/megan/rma2info/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::megan=6.21.7 diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index a1f2045a..e91af504 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -2,10 +2,10 @@ process MEGAN_RMA2INFO { tag "$meta.id" label 'process_single' - conda "bioconda::megan=6.21.7" + conda 'modules/nf-core/megan/rma2info/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - 'biocontainers/megan:6.21.7--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/megan:6.24.20--h9ee0642_0': + 'biocontainers/megan:6.24.20--h9ee0642_0' }" input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml index 710d9346..af3dd96c 100644 --- a/modules/nf-core/megan/rma2info/meta.yml +++ b/modules/nf-core/megan/rma2info/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: "['GPL >=3']" - input: - meta: type: map @@ -27,7 +26,6 @@ input: - megan_summary: type: boolean description: Specify whether to generate an MEGAN summary file - output: - meta: type: map @@ -46,6 +44,7 @@ output: type: file description: Optionally generated MEGAN summary file pattern: "*.megan" - authors: - "@jfy133" +maintainers: + - "@jfy133"