From 527ca85c2ea9af64d2d7f64498f61a9360d72bab Mon Sep 17 00:00:00 2001 From: James Fellows Yates <jfy133@gmail.com> Date: Thu, 26 Oct 2023 05:43:24 +0200 Subject: [PATCH 1/5] Update MEGAN --- modules/nf-core/megan/rma2info/environment.yml | 6 ++++++ modules/nf-core/megan/rma2info/main.nf | 6 +++--- modules/nf-core/megan/rma2info/meta.yml | 5 ++--- 3 files changed, 11 insertions(+), 6 deletions(-) create mode 100644 modules/nf-core/megan/rma2info/environment.yml 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" From 06d4360541eb92b14b85f7e5c293b6968b85ac8f Mon Sep 17 00:00:00 2001 From: James Fellows Yates <jfy133@gmail.com> Date: Thu, 26 Oct 2023 05:45:56 +0200 Subject: [PATCH 2/5] Update CHANGELOG --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ffd9c45..7eac5e3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,10 +12,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `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) +- [#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] Fix a null pointer exception 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] From aa4e9162f2567b4a30a8fb19a1846d418bfbd80f Mon Sep 17 00:00:00 2001 From: James Fellows Yates <jfy133@gmail.com> Date: Thu, 26 Oct 2023 05:46:48 +0200 Subject: [PATCH 3/5] Update Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7eac5e3b..e1c13b4b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) - [#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] Fix a null pointer exception error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` From 19865202a0077f3b351d2ebc8953a25430a9ec69 Mon Sep 17 00:00:00 2001 From: James Fellows Yates <jfy133@gmail.com> Date: Thu, 26 Oct 2023 05:47:32 +0200 Subject: [PATCH 4/5] Add PR links in CHANGELOG --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1c13b4b..c8bc3b12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,13 @@ 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] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ 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` From c22f719be45faa27c70cba324d74c1f915ef8149 Mon Sep 17 00:00:00 2001 From: James Fellows Yates <jfy133@gmail.com> Date: Thu, 26 Oct 2023 06:01:52 +0200 Subject: [PATCH 5/5] Add missing modules.json update --- modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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": {