From ff839b9da2b012f96f0305829922a4a3bbf38b63 Mon Sep 17 00:00:00 2001 From: louperelo Date: Thu, 13 Jul 2023 15:18:07 +0200 Subject: [PATCH 1/5] add Prokka to MultiQC --- assets/multiqc_config.yml | 4 ++++ workflows/funcscan.nf | 1 + 2 files changed, 5 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 356df32d..f5475e68 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -15,3 +15,7 @@ export_plots: true custom_logo: "nf-core-funcscan_logo_flat_light.png" custom_logo_url: https://nf-co.re/funcscan custom_logo_title: "nf-core/funcscan" + +## Tool specific configuration +prokka_fn_snames: True + diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf index 27168b24..71200511 100644 --- a/workflows/funcscan.nf +++ b/workflows/funcscan.nf @@ -273,6 +273,7 @@ workflow FUNCSCAN { ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) + if(params.annotation_tool=='prokka'){ch_multiqc_files = ch_multiqc_files.mix(PROKKA.out.txt.collect{it[1]}.ifEmpty([]))} MULTIQC ( ch_multiqc_files.collect(), From 7a696888f00da2735cf85aa7b7ddf75e22eefd20 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 14 Jul 2023 12:55:06 +0000 Subject: [PATCH 2/5] [automated] Fix linting with Prettier --- assets/multiqc_config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f5475e68..e72b21e2 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -18,4 +18,3 @@ custom_logo_title: "nf-core/funcscan" ## Tool specific configuration prokka_fn_snames: True - From e2a95fdd771cb413f33ab7d45bcac00afa1ce287 Mon Sep 17 00:00:00 2001 From: louperelo Date: Fri, 14 Jul 2023 15:12:58 +0200 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index da127edf..e879558c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.1.3dev - [unreleased] + +### `Added` + +- [#290](https://github.com/nf-core/funcscan/pull/290) Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133) +- [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output (by @louperelo) + + ### `Fixed` + + - [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz) + + ### `Dependencies` + + ### `Deprecated` + ## v1.1.2 - [2023-06-30] ### `Added` From 53cd340ae1311add8359e7762c8c3efbfca90f62 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 14 Jul 2023 13:59:39 +0000 Subject: [PATCH 4/5] [automated] Fix linting with Prettier --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8d0aba9b..1f5a1910 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,13 +11,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output (by @louperelo) - ### `Fixed` +### `Fixed` - - [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz) +- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz) - ### `Dependencies` +### `Dependencies` - ### `Deprecated` +### `Deprecated` ## v1.1.2 - [2023-06-30] From 74b59d06a7902bf63af00faddfaa8c797c92d9cc Mon Sep 17 00:00:00 2001 From: Louisa Perelo <44900284+louperelo@users.noreply.github.com> Date: Wed, 19 Jul 2023 11:08:50 +0200 Subject: [PATCH 5/5] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- workflows/funcscan.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf index 44f9c50e..17b7e6f8 100644 --- a/workflows/funcscan.nf +++ b/workflows/funcscan.nf @@ -282,7 +282,7 @@ workflow FUNCSCAN { ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - if(params.annotation_tool=='prokka'){ch_multiqc_files = ch_multiqc_files.mix(PROKKA.out.txt.collect{it[1]}.ifEmpty([]))} + if(params.annotation_tool=='prokka'){ch_multiqc_files = ch_multiqc_files.mix( PROKKA.out.txt.collect{it[1]}.ifEmpty([])) } MULTIQC ( ch_multiqc_files.collect(),