From b78b8e352eb57a6852bfb2c11624e6336363b7ee Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 30 Apr 2024 16:03:01 +0200 Subject: [PATCH 1/9] feat(wave): adding profile wave --- nextflow.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nextflow.config b/nextflow.config index 4f91dea55..4adb41fa3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,6 +248,12 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + wave { + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + singularity.ociAutoPull = true + } gitpod { executor.name = 'local' executor.cpus = 4 From d505e0d203af2230163e4a527ca7aa4c533cf6a6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 30 Apr 2024 16:04:56 +0200 Subject: [PATCH 2/9] sort --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 4adb41fa3..335f76794 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,10 +249,10 @@ profiles { charliecloud.enabled = false } wave { + singularity.ociAutoPull = true wave.enabled = true wave.freeze = true wave.strategy = 'conda,container' - singularity.ociAutoPull = true } gitpod { executor.name = 'local' From 4293c6dc9ecf0e6edfdad16b568c0ec1e0055ef7 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 30 Apr 2024 17:44:04 +0200 Subject: [PATCH 3/9] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 335f76794..eb91f8802 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,6 +249,7 @@ profiles { charliecloud.enabled = false } wave { + apptainer.ociAutoPull = true singularity.ociAutoPull = true wave.enabled = true wave.freeze = true From acf329ac703c29db150aa2fa3a5f2540dd463bae Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 30 Apr 2024 17:45:47 +0200 Subject: [PATCH 4/9] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a3ae93973..6c8a90fd6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -67,6 +67,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot +- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `wave` profile ### Parameters From a37afbfb190399b9d8158fcdd6beb49fb04825bc Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 May 2024 10:25:30 +0200 Subject: [PATCH 5/9] Apply suggestions from code review Co-authored-by: Paolo Di Tommaso --- nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index eb91f8802..5fb0be3c2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,12 +248,12 @@ profiles { shifter.enabled = false charliecloud.enabled = false } - wave { + seqera-containers { apptainer.ociAutoPull = true singularity.ociAutoPull = true wave.enabled = true wave.freeze = true - wave.strategy = 'conda,container' + wave.strategy = 'conda' } gitpod { executor.name = 'local' From d7b0037ac63948fde0044cb48207b5434d2882f4 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 May 2024 12:51:24 +0200 Subject: [PATCH 6/9] Update CHANGELOG.md Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 06fb8fcb6..9e505ebcd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -67,7 +67,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot -- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `wave` profile +- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `seqera-containers` profile - [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline ### Parameters From e0bcc22181bef3de70cf56a88ebac8120de8c3b9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 May 2024 13:06:42 +0200 Subject: [PATCH 7/9] Apply suggestions from code review --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e505ebcd..f9f420a91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -67,7 +67,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot -- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `seqera-containers` profile +- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `seqera_containers` profile - [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline ### Parameters diff --git a/nextflow.config b/nextflow.config index 5fb0be3c2..ca44d57f1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,7 +248,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false } - seqera-containers { + seqera_containers { apptainer.ociAutoPull = true singularity.ociAutoPull = true wave.enabled = true From 8b0e4a5575b68912f91fe55143e8a0080538d930 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 May 2024 18:08:21 +0200 Subject: [PATCH 8/9] Update usage.md --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 89ef06d8b..2ef13663e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -314,8 +314,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) -- `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). +- `seqera_containers` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) to build and pull from the Seqera public containers repository. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. From c27b63f30d3ec26ae97e1f167d07b546f784d759 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 May 2024 18:08:47 +0200 Subject: [PATCH 9/9] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 5e8a49980..7cc6a1a77 100644 --- a/nextflow.config +++ b/nextflow.config @@ -257,7 +257,7 @@ profiles { wave.strategy = 'conda,container' } seqera_containers { - apptainer.ociAutoPull = true + apptainer.ociAutoPull = true singularity.ociAutoPull = true wave.enabled = true wave.freeze = true