From 9e891d47197d3118bd03407fe2aac9139318872e Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 18 Dec 2024 11:47:42 +0100 Subject: [PATCH 1/3] Update rgi/main --- CHANGELOG.md | 1 + modules.json | 2 +- modules/nf-core/rgi/main/main.nf | 2 +- modules/nf-core/rgi/main/tests/main.nf.test.snap | 16 ++++++++-------- 4 files changed, 11 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b1fd07b7..4a8455c9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#427](https://github.com/nf-core/funcscan/pull/427) Fixed the AMP reference database issues reported by users, due to non-ASCII characters. (by @darcy220606) +- [#430](https://github.com/nf-core/funcscan/pull/430) Updated `rgi/main` module to fix incorrect variable name. (by @amizeranschi and @jasmezz) ### `Dependencies` diff --git a/modules.json b/modules.json index 3dd4848b..24ac4605 100644 --- a/modules.json +++ b/modules.json @@ -192,7 +192,7 @@ }, "rgi/main": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41623bcb962bd02d1a45ad81c1853547ebd26f5f", "installed_by": ["modules"] }, "seqkit/seq": { diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index ba05358a..287875fa 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -25,7 +25,7 @@ process RGI_MAIN { script: def args = task.ext.args ?: '' // This customizes the command: rgi load - def args2 = task.ext.args ?: '' // This customizes the command: rgi main + def args2 = task.ext.args2 ?: '' // This customizes the command: rgi main def prefix = task.ext.prefix ?: "${meta.id}" def load_wildcard = "" diff --git a/modules/nf-core/rgi/main/tests/main.nf.test.snap b/modules/nf-core/rgi/main/tests/main.nf.test.snap index a8dc1d61..35b4f7cf 100644 --- a/modules/nf-core/rgi/main/tests/main.nf.test.snap +++ b/modules/nf-core/rgi/main/tests/main.nf.test.snap @@ -81,15 +81,15 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-19T22:51:36.047807514" + "timestamp": "2024-12-10T13:33:59.209306934" }, "rgi/main - haemophilus_influenzae - genome_fna_gz": { "content": [ [ - "versions.yml:md5,a9f89e3bebd538efa07bcbe9fe1ba37a" + "versions.yml:md5,306dec3569e66a74bff07184f2f801ec" ], [ [ @@ -131,13 +131,13 @@ "6.0.3" ], [ - "3.2.9" + "3.3.0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-19T22:51:14.372178941" + "timestamp": "2024-12-10T13:33:40.479165988" } } \ No newline at end of file From 2531f7d2b5142607efa1bf8635ddff542f3e84e8 Mon Sep 17 00:00:00 2001 From: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:03:03 +0000 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a8455c9..a27c12d3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#421](https://github.com/nf-core/funcscan/pull/421) Updated to nf-core template 3.0.2 (by @jfy133) +- [#421](https://github.com/nf-core/funcscan/pull/421) Updated to nf-core template 3.0.2. (by @jfy133) - [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606) +- [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz) ### `Fixed` From 9541325b30c453ba3c88397e3a3d1959dc0d0097 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Thu, 19 Dec 2024 16:58:09 +0100 Subject: [PATCH 3/3] Update snapshot (due to CARD database update) --- tests/test_preannotated.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_preannotated.nf.test.snap b/tests/test_preannotated.nf.test.snap index e53c7215..82ab3487 100644 --- a/tests/test_preannotated.nf.test.snap +++ b/tests/test_preannotated.nf.test.snap @@ -143,9 +143,9 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66", - "sample_2.txt:md5,0e652d35ef6e9272aa194b55db609e75", - "sample_3.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66" + "sample_1.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955", + "sample_2.txt:md5,cc4ae1fb9e0d5f79ef5105d640c7b748", + "sample_3.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955" ], "meta": { "nf-test": "0.9.0",