From 03cc72a106be575c95322a9e02685448f52881b5 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 24 May 2023 23:39:43 +0200 Subject: [PATCH 01/10] Version bump --- CHANGELOG.md | 10 ++++++++++ nextflow.config | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b7afdbd..3f316ef3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ 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). +## v1.1.2dev - [unreleased] + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v1.1.1 - [2023-05-24] ### `Added` diff --git a/nextflow.config b/nextflow.config index 083b6d2f..43c84887 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.1.1' + version = '1.1.2dev' doi = '10.5281/zenodo.7643099' } From e9be867970e0fb70250b3f6c0849ef053d1d4bf1 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Thu, 25 May 2023 12:26:28 +0100 Subject: [PATCH 02/10] Hotfix: docker.registry outside of docker profile --- nextflow.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nextflow.config b/nextflow.config index 43c84887..67a151e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -350,6 +350,12 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set default registry for Docker and Podman independent of -profile +// Will not be used unless Docker / Podman are enabled +// Set to your registry if you have a mirror of containers +docker.registry = 'quay.io' +podman.registry = 'quay.io' + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true From 61df21400188cb90ba1e7a60cf30e9821c980d13 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 25 May 2023 13:22:34 +0100 Subject: [PATCH 03/10] Remove other occurences of docker.registry --- nextflow.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 67a151e5..15e90338 100644 --- a/nextflow.config +++ b/nextflow.config @@ -259,7 +259,6 @@ profiles { docker { conda.enabled = false docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -283,7 +282,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false From 44358fbdd8b73a4b39fb8aa4aab28da49b71ec23 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 29 Jun 2023 09:50:20 +0200 Subject: [PATCH 04/10] Add changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f316ef3..0f8c9802 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#279](https://github.com/nf-core/funcscan/pull/279) Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot) + ### `Dependencies` ### `Deprecated` From a9b7ca3dc0d512739e4353e08571f38b6d065fab Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 29 Jun 2023 09:51:24 +0200 Subject: [PATCH 05/10] Bump version for minor release --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0f8c9802..5e841bd4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.1.2dev - [unreleased] +## v1.1.2 - [2023-06-29] ### `Added` diff --git a/nextflow.config b/nextflow.config index 15e90338..0033018a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.1.2dev' + version = '1.1.2' doi = '10.5281/zenodo.7643099' } From b1cf106119c670562eac43989affd9cac39d2d0c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 29 Jun 2023 10:21:44 +0200 Subject: [PATCH 06/10] Update nextflow.config Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 0033018a..a9e49e85 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.1.2' + version = '1.1.2' doi = '10.5281/zenodo.7643099' } From bbf7f4aa2ae12860e2318bc607134178fc4eb44e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 29 Jun 2023 11:39:19 +0200 Subject: [PATCH 07/10] Update CHANGELOG.md Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e841bd4..748ceb4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#279](https://github.com/nf-core/funcscan/pull/279) Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot) +- [#279](https://github.com/nf-core/funcscan/pull/279) Fix docker/podman registry definition for tower compatibility. (fix by @adamrtalbot) ### `Dependencies` From 678d6ac06b0ae66c21bf5a13341f1bf5d07d8ca5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 29 Jun 2023 12:46:48 +0200 Subject: [PATCH 08/10] Update base.config --- conf/base.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index c517364b..62690e52 100644 --- a/conf/base.config +++ b/conf/base.config @@ -114,7 +114,8 @@ process { withName: DEEPARG_DOWNLOADDATA { memory = { check_max( 2.GB * task.attempt, 'memory' ) } - cpus = 1 + cpus = 1 + time = { check_max( 2.h * task.attempt, 'time' ) } } withName: DEEPARG_PREDICT { From ae0ec8a7df9b5a84e69946558cf6a22f1cce6fe6 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 29 Jun 2023 13:07:55 +0200 Subject: [PATCH 09/10] Update conf/base.config --- conf/base.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 62690e52..d689625f 100644 --- a/conf/base.config +++ b/conf/base.config @@ -114,7 +114,7 @@ process { withName: DEEPARG_DOWNLOADDATA { memory = { check_max( 2.GB * task.attempt, 'memory' ) } - cpus = 1 + cpus = 1 time = { check_max( 2.h * task.attempt, 'time' ) } } From 461784be9de11e2bbb5defd046ec562b350bbc96 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 30 Jun 2023 08:41:59 +0200 Subject: [PATCH 10/10] Apply suggestions from code review [skip ci] --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 748ceb4a..da127edf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,13 @@ 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). -## v1.1.2 - [2023-06-29] +## v1.1.2 - [2023-06-30] ### `Added` ### `Fixed` -- [#279](https://github.com/nf-core/funcscan/pull/279) Fix docker/podman registry definition for tower compatibility. (fix by @adamrtalbot) +- [#279](https://github.com/nf-core/funcscan/pull/279) Fix docker/podman registry definition for tower compatibility. (♥️ to sunitj for reporting, fix by @adamrtalbot) ### `Dependencies`