From 7093410b920040f5a6ccb1d0204eb8c654af243b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?= <58640615+LouisLeNezet@users.noreply.github.com> Date: Mon, 3 Mar 2025 16:05:28 +0100 Subject: [PATCH 1/4] Update main.nf --- .../utils_nfcore_pipeline_pipeline/main.nf | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 06faf35d7..4908e2109 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -9,15 +9,7 @@ */ {% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema'{% endif %} -{%- if email %} -include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' -{%- endif %} -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -{%- if adaptivecard or slackreport %} -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' -{%- endif %} include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -118,6 +110,15 @@ workflow PIPELINE_INITIALISATION { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { paramsSummaryMap } from 'plugin/nf-schema' +{%- if email %} +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +{%- endif %} +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +{%- if adaptivecard or slackreport %} +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +{%- endif %} + workflow PIPELINE_COMPLETION { take: From 6796c5c2539a03579bfeeb4d981ab783f517f36a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 3 Mar 2025 15:08:14 +0000 Subject: [PATCH 2/4] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 40a25cba0..23a209da7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ - chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473)) - chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470)) +- Move import in `utils_nfcore_phaseimpute_pipeline` ([#3476](https://github.com/nf-core/tools/pull/3476)) ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27] From b80ab4f45e70d914d9d4dace4059c8e2fda538ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?= <58640615+LouisLeNezet@users.noreply.github.com> Date: Mon, 3 Mar 2025 16:09:24 +0100 Subject: [PATCH 3/4] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 23a209da7..630ad4c50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Remove the on `pull_request_target` trigger and `pull_request` types from the download test. Also drop `push` triggers on other CI tests. ([#3399](https://github.com/nf-core/tools/pull/3399)) - Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396)) - Add Bluesky badge to readme ([#3475](https://github.com/nf-core/tools/pull/3475)) +- Move import in `utils_nfcore_phaseimpute_pipeline` next to using workflow ([#3476](https://github.com/nf-core/tools/pull/3476)) ### Linting From f6b0db7ef232627a1c1588a4940c96ff358aa574 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?= <58640615+LouisLeNezet@users.noreply.github.com> Date: Mon, 3 Mar 2025 16:18:08 +0100 Subject: [PATCH 4/4] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 630ad4c50..d3912cb05 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,7 +39,6 @@ - chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473)) - chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470)) -- Move import in `utils_nfcore_phaseimpute_pipeline` ([#3476](https://github.com/nf-core/tools/pull/3476)) ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]