From 20b824d3f65fa95a9385b903bbe187ae190a8255 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 26 Apr 2024 12:04:24 +0200 Subject: [PATCH 01/26] Add charliecloud.registry --- nf_core/pipeline-template/nextflow.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 17e75f18a4..f097cc2ff6 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -184,11 +184,11 @@ profiles { // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Singularity are enabled // Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' - +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Nextflow plugins plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet From 97bfc217fa02fef86c36100331fa8b27a6042c5b Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 26 Apr 2024 13:17:06 +0200 Subject: [PATCH 02/26] Update comment, add newline --- nf_core/pipeline-template/nextflow.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index f90fc546f6..cbc98cb022 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -180,14 +180,15 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers apptainer.registry = 'quay.io' docker.registry = 'quay.io' podman.registry = 'quay.io' singularity.registry = 'quay.io' charliecloud.registry = 'quay.io' + // Nextflow plugins plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet From 5e611c8ff68824836b487a9bfd4153e6c2db78fd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 13 May 2024 10:42:19 +0200 Subject: [PATCH 03/26] add GHA to post comment about outdated template version --- .../.github/workflows/linting.yml | 8 +++- .../workflows/template_version_comment.yml | 42 +++++++++++++++++++ 2 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 nf_core/pipeline-template/.github/workflows/template_version_comment.yml diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index b2cde075fe..229aa9f652 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -41,10 +41,16 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core lint env: diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml new file mode 100644 index 0000000000..2f49ab1269 --- /dev/null +++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml @@ -0,0 +1,42 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Read template version from .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: pip list --outdated | grep nf-core + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + message: | + ## :warning: New nf-core template version available + + Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + Please update your pipeline to the latest version. + + For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). From 7c1bb8a17ebe4b6e3a8afe27e4c78bdc42df01fb Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 13 May 2024 08:45:47 +0000 Subject: [PATCH 04/26] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f46a265cc..ba1d7da108 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,8 @@ ### Linting +- Template: Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978)) + ### Download ### Components From 940b3841e94b8368b5827aa356010e8700f3ead7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 13 May 2024 11:33:16 +0200 Subject: [PATCH 05/26] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .../.github/workflows/template_version_comment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml index 2f49ab1269..e21283309d 100644 --- a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml @@ -31,10 +31,10 @@ jobs: if: | ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' with: - repo-token: ${{ secrets.GITHUB_TOKEN }} + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: New nf-core template version available + ## :warning: Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. Please update your pipeline to the latest version. From c448406b5e8ddae9d2c618db0ca464dbc97e7cb2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 15 May 2024 14:21:04 +0200 Subject: [PATCH 06/26] update template according to PR 5281 in modules --- nf_core/module-template/tests/main.nf.test.j2 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/module-template/tests/main.nf.test.j2 b/nf_core/module-template/tests/main.nf.test.j2 index f31e92d659..1f70df64b0 100644 --- a/nf_core/module-template/tests/main.nf.test.j2 +++ b/nf_core/module-template/tests/main.nf.test.j2 @@ -28,10 +28,10 @@ nextflow_process { {% if has_meta %} input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] {%- else %} - input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) {%- endif %} """ } @@ -60,10 +60,10 @@ nextflow_process { {% if has_meta %} input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] {%- else %} - input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) {%- endif %} """ } From 4ca14b448471dd365c13b41dbe13c46254d24b2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 15 May 2024 14:27:11 +0200 Subject: [PATCH 07/26] update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e130d3c37b..02dc68cae2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # nf-core/tools: Changelog +### Template + +- Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985)) + ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] ### Template From 51447b27afc787075048b0deb51d2737dcc43062 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 15 May 2024 14:29:08 +0200 Subject: [PATCH 08/26] Apply suggestions from code review --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0338ec0bae..52b4d57350 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,5 @@ # nf-core/tools: Changelog - ## v2.14.2dev ### Template From 515ef02739a2da37701964c96798e2c2c1e15e8a Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Mon, 20 May 2024 14:24:55 +1000 Subject: [PATCH 09/26] Fix README.md admonition --- nf_core/pipeline-template/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index e6351b0c6f..ad0914f98d 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -80,8 +80,7 @@ nextflow run {{ name }} \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). {% if is_nfcore -%} From a70f8a80316bf580c408fef925ef01652191b912 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 20 May 2024 17:02:32 +0200 Subject: [PATCH 10/26] Update website docs link --- nf_core/pipeline-template/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index ad0914f98d..feece399b5 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -80,7 +80,7 @@ nextflow run {{ name }} \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). {% if is_nfcore -%} From 1d0d69135454ea080abee18a32636eb50bd8d2fb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 21 May 2024 12:33:10 +0200 Subject: [PATCH 11/26] update test after updating bwa/mem module --- tests/components/generate_snapshot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/components/generate_snapshot.py b/tests/components/generate_snapshot.py index 3176569ec8..a5a8eaba39 100644 --- a/tests/components/generate_snapshot.py +++ b/tests/components/generate_snapshot.py @@ -91,7 +91,7 @@ def test_update_snapshot_module(self): snap_content = json.load(fh) original_timestamp = snap_content["Single-End"]["timestamp"] # delete the timestamp in json - snap_content["Single-End"]["content"][0]["0"][0][1] = "" + snap_content["Single-End"]["timestamp"] = "" with open(snap_path, "w") as fh: json.dump(snap_content, fh) snap_generator = ComponentsTest( From 49896ff1f42ab44b97f64f22c63455256473d214 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 21 May 2024 13:20:12 +0000 Subject: [PATCH 12/26] Add no clobber and put bash options on their own line --- nf_core/pipeline-template/nextflow.config | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 7648a5ebc3..4d1701bf76 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -220,8 +220,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false From 589265e68164bf024654f83255e36509d425dc60 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 21 May 2024 13:23:11 +0000 Subject: [PATCH 13/26] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16573a91e2..06d8e1b5c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974)) - Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) +- Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From e6b089b6e14ea2d8a1dd86a1b8454aec02e46b99 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 15 May 2024 22:40:15 +0000 Subject: [PATCH 14/26] Update python:3.12-slim Docker digest to afc139a --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ae3a4e1a3d..fe4162b4fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:2be8daddbb82756f7d1f2c7ece706aadcb284bf6ab6d769ea695cc3ed6016743 +FROM python:3.12-slim@sha256:afc139a0a640942491ec481ad8dda10f2c5b753f5c969393b12480155fe15a63 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 2220a743aafea764f97b8a7b186888e689b7b7b3 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 23 May 2024 12:30:23 +0200 Subject: [PATCH 15/26] update minimal textual version and snapshots accordingly --- requirements.txt | 2 +- tests/__snapshots__/test_create_app.ambr | 3031 +++++++++++----------- 2 files changed, 1516 insertions(+), 1517 deletions(-) diff --git a/requirements.txt b/requirements.txt index acf30f491d..44241e0d95 100644 --- a/requirements.txt +++ b/requirements.txt @@ -21,6 +21,6 @@ requests_cache rich-click>=1.6.1 rich>=13.3.1 tabulate -textual>=0.47.1 +textual>=0.63.1 trogon pdiff diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index c486ec4f8f..f5a519b133 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -22,253 +22,254 @@ font-weight: 700; } - .terminal-1527309810-matrix { + .terminal-3833894853-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1527309810-title { + .terminal-3833894853-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1527309810-r1 { fill: #c5c8c6 } - .terminal-1527309810-r2 { fill: #e3e3e3 } - .terminal-1527309810-r3 { fill: #989898 } - .terminal-1527309810-r4 { fill: #e1e1e1 } - .terminal-1527309810-r5 { fill: #121212 } - .terminal-1527309810-r6 { fill: #0053aa } - .terminal-1527309810-r7 { fill: #dde8f3;font-weight: bold } - .terminal-1527309810-r8 { fill: #a5a5a5;font-style: italic; } - .terminal-1527309810-r9 { fill: #1e1e1e } - .terminal-1527309810-r10 { fill: #008139 } - .terminal-1527309810-r11 { fill: #e2e2e2 } - .terminal-1527309810-r12 { fill: #787878 } - .terminal-1527309810-r13 { fill: #b93c5b } - .terminal-1527309810-r14 { fill: #454a50 } - .terminal-1527309810-r15 { fill: #7ae998 } - .terminal-1527309810-r16 { fill: #e2e3e3;font-weight: bold } - .terminal-1527309810-r17 { fill: #0a180e;font-weight: bold } - .terminal-1527309810-r18 { fill: #000000 } - .terminal-1527309810-r19 { fill: #ddedf9 } + .terminal-3833894853-r1 { fill: #c5c8c6 } + .terminal-3833894853-r2 { fill: #e3e3e3 } + .terminal-3833894853-r3 { fill: #989898 } + .terminal-3833894853-r4 { fill: #e1e1e1 } + .terminal-3833894853-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3833894853-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-3833894853-r7 { fill: #1e1e1e } + .terminal-3833894853-r8 { fill: #008139 } + .terminal-3833894853-r9 { fill: #121212 } + .terminal-3833894853-r10 { fill: #e2e2e2 } + .terminal-3833894853-r11 { fill: #787878 } + .terminal-3833894853-r12 { fill: #b93c5b } + .terminal-3833894853-r13 { fill: #454a50 } + .terminal-3833894853-r14 { fill: #7ae998 } + .terminal-3833894853-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-3833894853-r16 { fill: #0a180e;font-weight: bold } + .terminal-3833894853-r17 { fill: #000000 } + .terminal-3833894853-r18 { fill: #fea62b;font-weight: bold } + .terminal-3833894853-r19 { fill: #a7a9ab } + .terminal-3833894853-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Basic details▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -298,256 +299,257 @@ font-weight: 700; } - .terminal-2230840552-matrix { + .terminal-170499771-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2230840552-title { + .terminal-170499771-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2230840552-r1 { fill: #c5c8c6 } - .terminal-2230840552-r2 { fill: #e3e3e3 } - .terminal-2230840552-r3 { fill: #989898 } - .terminal-2230840552-r4 { fill: #e1e1e1 } - .terminal-2230840552-r5 { fill: #121212 } - .terminal-2230840552-r6 { fill: #0053aa } - .terminal-2230840552-r7 { fill: #dde8f3;font-weight: bold } - .terminal-2230840552-r8 { fill: #a5a5a5;font-style: italic; } - .terminal-2230840552-r9 { fill: #1e1e1e } - .terminal-2230840552-r10 { fill: #0f4e2a } - .terminal-2230840552-r11 { fill: #0178d4 } - .terminal-2230840552-r12 { fill: #a7a7a7 } - .terminal-2230840552-r13 { fill: #787878 } - .terminal-2230840552-r14 { fill: #e2e2e2 } - .terminal-2230840552-r15 { fill: #b93c5b } - .terminal-2230840552-r16 { fill: #454a50 } - .terminal-2230840552-r17 { fill: #7ae998 } - .terminal-2230840552-r18 { fill: #e2e3e3;font-weight: bold } - .terminal-2230840552-r19 { fill: #0a180e;font-weight: bold } - .terminal-2230840552-r20 { fill: #000000 } - .terminal-2230840552-r21 { fill: #008139 } - .terminal-2230840552-r22 { fill: #ddedf9 } + .terminal-170499771-r1 { fill: #c5c8c6 } + .terminal-170499771-r2 { fill: #e3e3e3 } + .terminal-170499771-r3 { fill: #989898 } + .terminal-170499771-r4 { fill: #e1e1e1 } + .terminal-170499771-r5 { fill: #4ebf71;font-weight: bold } + .terminal-170499771-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-170499771-r7 { fill: #1e1e1e } + .terminal-170499771-r8 { fill: #0f4e2a } + .terminal-170499771-r9 { fill: #0178d4 } + .terminal-170499771-r10 { fill: #a7a7a7 } + .terminal-170499771-r11 { fill: #787878 } + .terminal-170499771-r12 { fill: #e2e2e2 } + .terminal-170499771-r13 { fill: #b93c5b } + .terminal-170499771-r14 { fill: #121212 } + .terminal-170499771-r15 { fill: #454a50 } + .terminal-170499771-r16 { fill: #7ae998 } + .terminal-170499771-r17 { fill: #e2e3e3;font-weight: bold } + .terminal-170499771-r18 { fill: #0a180e;font-weight: bold } + .terminal-170499771-r19 { fill: #000000 } + .terminal-170499771-r20 { fill: #008139 } + .terminal-170499771-r21 { fill: #fea62b;font-weight: bold } + .terminal-170499771-r22 { fill: #a7a9ab } + .terminal-170499771-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Basic details▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -577,253 +579,251 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Choose pipeline type▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊▎▊ - ▎       Choose "nf-core" if:       ▊▎       Choose "Custom" if:        ▊ - ▎▊▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ● You want your pipeline to be part of● Your pipeline will never be part of  - the nf-core communitynf-core - ● You think that there's an outside ● You want full control over all - chance that it ever could be part offeatures that are included from the  - nf-coretemplate (including those that are  - mandatory for nf-core). - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁Custom - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎                                 What's the difference?                                 ▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Choosing "nf-core" effectively pre-selects the following template features: - - ● GitHub Actions continuous-integration configuration files: - ▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) - ▪ Code formatting checks with Prettier - ▪ Auto-fix linting functionality using @nf-core-bot - ▪ Marking old issues as stale - ● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Choose pipeline type + + + + + Choose "nf-core" if:Choose "Custom" if: + + ● You want your pipeline to be part of the ● Your pipeline will never be part of  + nf-core communitynf-core + ● You think that there's an outside chance ● You want full control over all features  + that it ever could be part of nf-corethat are included from the template  + (including those that are mandatory for  + nf-core). + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Custom + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + What's the difference? + + Choosing "nf-core" effectively pre-selects the following template features: + + ● GitHub Actions continuous-integration configuration files: + ▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) + ▪ Code formatting checks with Prettier + ▪ Auto-fix linting functionality using @nf-core-bot + ▪ Marking old issues as stale + ● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -853,257 +853,257 @@ font-weight: 700; } - .terminal-3071202289-matrix { + .terminal-3598234483-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3071202289-title { + .terminal-3598234483-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3071202289-r1 { fill: #c5c8c6 } - .terminal-3071202289-r2 { fill: #e3e3e3 } - .terminal-3071202289-r3 { fill: #989898 } - .terminal-3071202289-r4 { fill: #e1e1e1 } - .terminal-3071202289-r5 { fill: #121212 } - .terminal-3071202289-r6 { fill: #0053aa } - .terminal-3071202289-r7 { fill: #dde8f3;font-weight: bold } - .terminal-3071202289-r8 { fill: #1e1e1e } - .terminal-3071202289-r9 { fill: #0178d4 } - .terminal-3071202289-r10 { fill: #454a50 } - .terminal-3071202289-r11 { fill: #e2e2e2 } - .terminal-3071202289-r12 { fill: #808080 } - .terminal-3071202289-r13 { fill: #e2e3e3;font-weight: bold } - .terminal-3071202289-r14 { fill: #000000 } - .terminal-3071202289-r15 { fill: #e4e4e4 } - .terminal-3071202289-r16 { fill: #14191f } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Template features▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline Hide help - ▊▁▁▁▁▁▁▁▁▎genomeswill be ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configured to  - use a copy of  - the most common  - reference genome - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most  - common reference genome files. - - By selecting this option, your pipeline will include a  - configuration file specifying the paths to these files. - - The required code to use these files will also be included in  - the template. When the pipeline user provides an appropriate  - genome key, the pipeline will automatically download the ▂▂ - required reference files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github CI The pipeline Show help▅▅ - ▊▁▁▁▁▁▁▁▁▎testswill include ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - several GitHub  - actions for  - Continuous  - Integration (CI) - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github The README.md Show help - ▊▁▁▁▁▁▁▁▁▎badgesfile of the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - pipeline will  - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Use reference The pipeline will Hide help + ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Add Github CI The pipeline will Show help + ▊▁▁▁▁▁▁▁▁▎testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing▄▄ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Add Github badgesThe README.md fileShow help + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackContinue + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode q Quit @@ -1133,252 +1133,252 @@ font-weight: 700; } - .terminal-1456849374-matrix { + .terminal-1869771697-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1456849374-title { + .terminal-1869771697-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1456849374-r1 { fill: #c5c8c6 } - .terminal-1456849374-r2 { fill: #e3e3e3 } - .terminal-1456849374-r3 { fill: #989898 } - .terminal-1456849374-r4 { fill: #e1e1e1 } - .terminal-1456849374-r5 { fill: #121212 } - .terminal-1456849374-r6 { fill: #0053aa } - .terminal-1456849374-r7 { fill: #dde8f3;font-weight: bold } - .terminal-1456849374-r8 { fill: #a5a5a5;font-style: italic; } - .terminal-1456849374-r9 { fill: #1e1e1e } - .terminal-1456849374-r10 { fill: #008139 } - .terminal-1456849374-r11 { fill: #e2e2e2 } - .terminal-1456849374-r12 { fill: #b93c5b } - .terminal-1456849374-r13 { fill: #454a50 } - .terminal-1456849374-r14 { fill: #7ae998 } - .terminal-1456849374-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-1456849374-r16 { fill: #0a180e;font-weight: bold } - .terminal-1456849374-r17 { fill: #000000 } - .terminal-1456849374-r18 { fill: #ddedf9 } + .terminal-1869771697-r1 { fill: #c5c8c6 } + .terminal-1869771697-r2 { fill: #e3e3e3 } + .terminal-1869771697-r3 { fill: #989898 } + .terminal-1869771697-r4 { fill: #e1e1e1 } + .terminal-1869771697-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1869771697-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-1869771697-r7 { fill: #1e1e1e } + .terminal-1869771697-r8 { fill: #008139 } + .terminal-1869771697-r9 { fill: #e2e2e2 } + .terminal-1869771697-r10 { fill: #b93c5b } + .terminal-1869771697-r11 { fill: #454a50 } + .terminal-1869771697-r12 { fill: #7ae998 } + .terminal-1869771697-r13 { fill: #e2e3e3;font-weight: bold } + .terminal-1869771697-r14 { fill: #0a180e;font-weight: bold } + .terminal-1869771697-r15 { fill: #000000 } + .terminal-1869771697-r16 { fill: #fea62b;font-weight: bold } + .terminal-1869771697-r17 { fill: #a7a9ab } + .terminal-1869771697-r18 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Final details▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - - First version of the pipelinePath to the output directory where the pipeline  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created - ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackFinish - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Final details + + + + First version of the pipelinePath to the output directory where the pipeline  + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created + ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackFinish + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1408,260 +1408,262 @@ font-weight: 700; } - .terminal-436990287-matrix { + .terminal-1242773313-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-436990287-title { + .terminal-1242773313-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-436990287-r1 { fill: #c5c8c6 } - 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.terminal-436990287-r23 { fill: #0a180e;font-weight: bold } - .terminal-436990287-r24 { fill: #dde6ed;font-weight: bold } - .terminal-436990287-r25 { fill: #001541 } - .terminal-436990287-r26 { fill: #ddedf9 } + .terminal-1242773313-r1 { fill: #c5c8c6 } + .terminal-1242773313-r2 { fill: #e3e3e3 } + .terminal-1242773313-r3 { fill: #989898 } + .terminal-1242773313-r4 { fill: #e1e1e1 } + .terminal-1242773313-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1242773313-r6 { fill: #18954b } + .terminal-1242773313-r7 { fill: #e2e2e2 } + .terminal-1242773313-r8 { fill: #e2e2e2;font-style: italic; } + .terminal-1242773313-r9 { fill: #e2e2e2;font-style: italic;;text-decoration: underline; } + .terminal-1242773313-r10 { fill: #a5a5a5;font-style: italic; } + .terminal-1242773313-r11 { fill: #1e1e1e } + .terminal-1242773313-r12 { fill: #008139 } + .terminal-1242773313-r13 { fill: #454a50 } + .terminal-1242773313-r14 { fill: #787878 } + .terminal-1242773313-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1242773313-r16 { fill: #000000 } + .terminal-1242773313-r17 { fill: #b93c5b } + .terminal-1242773313-r18 { fill: #e2e2e2;font-weight: bold } + .terminal-1242773313-r19 { fill: #969696;font-weight: bold } + .terminal-1242773313-r20 { fill: #808080 } + .terminal-1242773313-r21 { fill: #7ae998 } + .terminal-1242773313-r22 { fill: #507bb3 } + .terminal-1242773313-r23 { fill: #0a180e;font-weight: bold } + .terminal-1242773313-r24 { fill: #dde6ed;font-weight: bold } + .terminal-1242773313-r25 { fill: #001541 } + .terminal-1242773313-r26 { fill: #fea62b;font-weight: bold } + .terminal-1242773313-r27 { fill: #a7a9ab } + .terminal-1242773313-r28 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Create GitHub repository▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Now that we have created a new pipeline locally, we can create a new GitHub repository and  - push the code to it. - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user - ▌account. A core-team member will be able to transfer the repo to nf-core once the  - ▌development has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + ▌💡 Found GitHub username in local GitHub CLI config + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ + ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + +  d Toggle dark mode q Quit @@ -1691,255 +1693,254 @@ font-weight: 700; } - .terminal-2484211597-matrix { + .terminal-396289429-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2484211597-title { + .terminal-396289429-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2484211597-r1 { fill: #c5c8c6 } - .terminal-2484211597-r2 { fill: #e3e3e3 } - .terminal-2484211597-r3 { fill: #989898 } - .terminal-2484211597-r4 { fill: #e1e1e1 } - .terminal-2484211597-r5 { fill: #121212 } - .terminal-2484211597-r6 { fill: #0053aa } - .terminal-2484211597-r7 { fill: #dde8f3;font-weight: bold } - .terminal-2484211597-r8 { fill: #98e024 } - .terminal-2484211597-r9 { fill: #626262 } - .terminal-2484211597-r10 { fill: #9d65ff } - .terminal-2484211597-r11 { fill: #fd971f } - .terminal-2484211597-r12 { fill: #4ebf71;font-weight: bold } - .terminal-2484211597-r13 { fill: #d2d2d2 } - .terminal-2484211597-r14 { fill: #82aaff } - .terminal-2484211597-r15 { fill: #eeffff } - .terminal-2484211597-r16 { fill: #4ebf71 } - .terminal-2484211597-r17 { fill: #e2e2e2 } - .terminal-2484211597-r18 { fill: #969696;font-weight: bold } - .terminal-2484211597-r19 { fill: #7ae998 } - .terminal-2484211597-r20 { fill: #008139 } - .terminal-2484211597-r21 { fill: #ddedf9 } + .terminal-396289429-r1 { fill: #c5c8c6 } + .terminal-396289429-r2 { fill: #e3e3e3 } + .terminal-396289429-r3 { fill: #989898 } + .terminal-396289429-r4 { fill: #e1e1e1 } + .terminal-396289429-r5 { fill: #4ebf71;font-weight: bold } + .terminal-396289429-r6 { fill: #98e024 } + .terminal-396289429-r7 { fill: #626262 } + .terminal-396289429-r8 { fill: #9d65ff } + .terminal-396289429-r9 { fill: #fd971f } + .terminal-396289429-r10 { fill: #d2d2d2 } + .terminal-396289429-r11 { fill: #82aaff } + .terminal-396289429-r12 { fill: #eeffff } + .terminal-396289429-r13 { fill: #18954b } + .terminal-396289429-r14 { fill: #e2e2e2 } + .terminal-396289429-r15 { fill: #969696;font-weight: bold } + .terminal-396289429-r16 { fill: #7ae998 } + .terminal-396289429-r17 { fill: #008139 } + .terminal-396289429-r18 { fill: #fea62b;font-weight: bold } + .terminal-396289429-r19 { fill: #a7a9ab } + .terminal-396289429-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎HowTo create a GitHub repository▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - - If you would like to create the GitHub repository later, you can do it manually by following - these steps: - -  1. Create a new GitHub repository -  2. Add the remote to your local repository: - - - cd<pipeline_directory> - gitremoteaddorigingit@github.com:<username>/<repo_name>.git - - -  3. Push the code to the remote: - - - gitpush--allorigin - - - ▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + HowTo create a GitHub repository + + + +                                           ,--./,-. +           ___     __   __   __   ___     /,-._.--~\  +     |\ | |__  __ /  ` /  \ |__) |__         }  { +     | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                           `._,._,' + + If you would like to create the GitHub repository later, you can do it manually by following  + these steps: + +  1. Create a new GitHub repository +  2. Add the remote to your local repository: + + + cd<pipeline_directory> + gitremoteaddorigingit@github.com:<username>/<repo_name>.git + + +  3. Push the code to the remote: + + + gitpush--allorigin + + + ▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1969,248 +1970,247 @@ font-weight: 700; } - .terminal-4165331380-matrix { + .terminal-3492397142-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4165331380-title { + .terminal-3492397142-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4165331380-r1 { fill: #c5c8c6 } - .terminal-4165331380-r2 { fill: #e3e3e3 } - .terminal-4165331380-r3 { fill: #989898 } - .terminal-4165331380-r4 { fill: #e1e1e1 } - .terminal-4165331380-r5 { fill: #121212 } - .terminal-4165331380-r6 { fill: #0053aa } - .terminal-4165331380-r7 { fill: #dde8f3;font-weight: bold } - .terminal-4165331380-r8 { fill: #7ae998 } - .terminal-4165331380-r9 { fill: #507bb3 } - .terminal-4165331380-r10 { fill: #4ebf71;font-weight: bold } - .terminal-4165331380-r11 { fill: #dde6ed;font-weight: bold } - .terminal-4165331380-r12 { fill: #008139 } - .terminal-4165331380-r13 { fill: #001541 } - .terminal-4165331380-r14 { fill: #ddedf9 } + .terminal-3492397142-r1 { fill: #c5c8c6 } + .terminal-3492397142-r2 { fill: #e3e3e3 } + .terminal-3492397142-r3 { fill: #989898 } + .terminal-3492397142-r4 { fill: #e1e1e1 } + .terminal-3492397142-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3492397142-r6 { fill: #7ae998 } + .terminal-3492397142-r7 { fill: #507bb3 } + .terminal-3492397142-r8 { fill: #dde6ed;font-weight: bold } + .terminal-3492397142-r9 { fill: #008139 } + .terminal-3492397142-r10 { fill: #001541 } + .terminal-3492397142-r11 { fill: #fea62b;font-weight: bold } + .terminal-3492397142-r12 { fill: #a7a9ab } + .terminal-3492397142-r13 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Create GitHub repository▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - After creating the pipeline template locally, we can create a GitHub repository and push the - code to it. - - Do you want to create a GitHub repository? - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + + After creating the pipeline template locally, we can create a GitHub repository and push the  + code to it. + + Do you want to create a GitHub repository? + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -2240,254 +2240,254 @@ font-weight: 700; } - .terminal-3459022791-matrix { + .terminal-4082092032-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3459022791-title { + .terminal-4082092032-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3459022791-r1 { fill: #c5c8c6 } - .terminal-3459022791-r2 { fill: #e3e3e3 } - .terminal-3459022791-r3 { fill: #989898 } - .terminal-3459022791-r4 { fill: #e1e1e1 } - .terminal-3459022791-r5 { fill: #121212 } - .terminal-3459022791-r6 { fill: #0053aa } - .terminal-3459022791-r7 { fill: #dde8f3;font-weight: bold } - .terminal-3459022791-r8 { fill: #1e1e1e } - .terminal-3459022791-r9 { fill: #507bb3 } - .terminal-3459022791-r10 { fill: #e2e2e2 } - .terminal-3459022791-r11 { fill: #808080 } - .terminal-3459022791-r12 { fill: #dde6ed;font-weight: bold } - .terminal-3459022791-r13 { fill: #001541 } - .terminal-3459022791-r14 { fill: #454a50 } - .terminal-3459022791-r15 { fill: #7ae998 } - .terminal-3459022791-r16 { fill: #e2e3e3;font-weight: bold } - .terminal-3459022791-r17 { fill: #0a180e;font-weight: bold } - .terminal-3459022791-r18 { fill: #000000 } - .terminal-3459022791-r19 { fill: #008139 } - .terminal-3459022791-r20 { fill: #ddedf9 } + .terminal-4082092032-r1 { fill: #c5c8c6 } + .terminal-4082092032-r2 { fill: #e3e3e3 } + .terminal-4082092032-r3 { fill: #989898 } + .terminal-4082092032-r4 { fill: #e1e1e1 } + .terminal-4082092032-r5 { fill: #4ebf71;font-weight: bold } + .terminal-4082092032-r6 { fill: #1e1e1e } + .terminal-4082092032-r7 { fill: #507bb3 } + .terminal-4082092032-r8 { fill: #e2e2e2 } + .terminal-4082092032-r9 { fill: #808080 } + .terminal-4082092032-r10 { fill: #dde6ed;font-weight: bold } + .terminal-4082092032-r11 { fill: #001541 } + .terminal-4082092032-r12 { fill: #454a50 } + .terminal-4082092032-r13 { fill: #7ae998 } + .terminal-4082092032-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-4082092032-r15 { fill: #0a180e;font-weight: bold } + .terminal-4082092032-r16 { fill: #000000 } + .terminal-4082092032-r17 { fill: #008139 } + .terminal-4082092032-r18 { fill: #fea62b;font-weight: bold } + .terminal-4082092032-r19 { fill: #a7a9ab } + .terminal-4082092032-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Template features▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline willShow help - ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github CI The pipeline willShow help - ▊▁▁▁▁▁▁▁▁▎testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions  - for Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github badgesThe README.md Show help - ▊▁▁▁▁▁▁▁▁▎file of the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - pipeline will  - include GitHub  - badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add configurationThe pipeline willShow help - ▊▁▁▁▁▁▁▁▁▎filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom - parameters  - requried to run  - nf-core pipelines - at different  - institutions - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Use reference The pipeline will Show help + ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Add Github CI testsThe pipeline will Show help + ▊▁▁▁▁▁▁▁▁▎include several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for  + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Add Github badgesThe README.md file Show help + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include GitHub + badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Add configuration The pipeline will Show help + ▊▁▁▁▁▁▁▁▁▎filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles containing + custom parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackContinue + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode q Quit @@ -2517,254 +2517,254 @@ font-weight: 700; } - .terminal-461754173-matrix { + .terminal-1639960877-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-461754173-title { + .terminal-1639960877-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-461754173-r1 { fill: #c5c8c6 } - .terminal-461754173-r2 { fill: #e3e3e3 } - .terminal-461754173-r3 { fill: #989898 } - .terminal-461754173-r4 { fill: #e1e1e1 } - .terminal-461754173-r5 { fill: #121212 } - .terminal-461754173-r6 { fill: #0053aa } - .terminal-461754173-r7 { fill: #dde8f3;font-weight: bold } - .terminal-461754173-r8 { fill: #1e1e1e } - .terminal-461754173-r9 { fill: #507bb3 } - .terminal-461754173-r10 { fill: #e2e2e2 } - .terminal-461754173-r11 { fill: #808080 } - .terminal-461754173-r12 { fill: #dde6ed;font-weight: bold } - .terminal-461754173-r13 { fill: #001541 } - .terminal-461754173-r14 { fill: #454a50 } - .terminal-461754173-r15 { fill: #7ae998 } - .terminal-461754173-r16 { fill: #e2e3e3;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Template features▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline willShow help - ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the - most common  - reference genome  - files from  - iGenomes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎Use reference The pipeline will Show help + ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from iGenomes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackContinue + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode q Quit @@ -2794,256 +2794,256 @@ font-weight: 700; } - .terminal-2179958535-matrix { + .terminal-2625911002-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2179958535-title { + .terminal-2625911002-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2179958535-r1 { fill: #c5c8c6 } - .terminal-2179958535-r2 { fill: #e3e3e3 } - .terminal-2179958535-r3 { fill: #989898 } - .terminal-2179958535-r4 { fill: #e1e1e1 } - .terminal-2179958535-r5 { fill: #121212 } - .terminal-2179958535-r6 { fill: #0053aa } - .terminal-2179958535-r7 { fill: #dde8f3;font-weight: bold } - .terminal-2179958535-r8 { fill: #a5a5a5;font-style: italic; } - .terminal-2179958535-r9 { fill: #1e1e1e } - .terminal-2179958535-r10 { fill: #0f4e2a } - .terminal-2179958535-r11 { fill: #7b3042 } - .terminal-2179958535-r12 { fill: #a7a7a7 } - .terminal-2179958535-r13 { fill: #787878 } - .terminal-2179958535-r14 { fill: #e2e2e2 } - .terminal-2179958535-r15 { fill: #b93c5b } - .terminal-2179958535-r16 { fill: #454a50 } - .terminal-2179958535-r17 { fill: #166d39 } - .terminal-2179958535-r18 { fill: #e2e3e3;font-weight: bold } - .terminal-2179958535-r19 { fill: #3c8b54;font-weight: bold } - .terminal-2179958535-r20 { fill: #000000 } - .terminal-2179958535-r21 { fill: #5aa86f } - .terminal-2179958535-r22 { fill: #ddedf9 } + .terminal-2625911002-r1 { fill: #c5c8c6 } + .terminal-2625911002-r2 { fill: #e3e3e3 } + .terminal-2625911002-r3 { fill: #989898 } + .terminal-2625911002-r4 { fill: #e1e1e1 } + .terminal-2625911002-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2625911002-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-2625911002-r7 { fill: #1e1e1e } + .terminal-2625911002-r8 { fill: #0f4e2a } + .terminal-2625911002-r9 { fill: #7b3042 } + .terminal-2625911002-r10 { fill: #a7a7a7 } + .terminal-2625911002-r11 { fill: #787878 } + .terminal-2625911002-r12 { fill: #e2e2e2 } + .terminal-2625911002-r13 { fill: #b93c5b } + .terminal-2625911002-r14 { fill: #454a50 } + .terminal-2625911002-r15 { fill: #166d39 } + .terminal-2625911002-r16 { fill: #e2e3e3;font-weight: bold } + .terminal-2625911002-r17 { fill: #3c8b54;font-weight: bold } + .terminal-2625911002-r18 { fill: #000000 } + .terminal-2625911002-r19 { fill: #5aa86f } + .terminal-2625911002-r20 { fill: #fea62b;font-weight: bold } + .terminal-2625911002-r21 { fill: #a7a9ab } + .terminal-2625911002-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Basic details▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Must be lowercase without  + punctuation. + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -3073,254 +3073,253 @@ font-weight: 700; } - .terminal-1144763792-matrix { + .terminal-3787732750-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1144763792-title { + .terminal-3787732750-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1144763792-r1 { fill: #c5c8c6 } - .terminal-1144763792-r2 { fill: #e3e3e3 } - .terminal-1144763792-r3 { fill: #989898 } - .terminal-1144763792-r4 { fill: #98e024 } - .terminal-1144763792-r5 { fill: #626262 } - .terminal-1144763792-r6 { fill: #9d65ff } - .terminal-1144763792-r7 { fill: #fd971f } - .terminal-1144763792-r8 { fill: #e1e1e1 } - .terminal-1144763792-r9 { fill: #121212 } - .terminal-1144763792-r10 { fill: #0053aa } - .terminal-1144763792-r11 { fill: #dde8f3;font-weight: bold } - .terminal-1144763792-r12 { fill: #e1e1e1;text-decoration: underline; } - .terminal-1144763792-r13 { fill: #4ebf71 } - .terminal-1144763792-r14 { fill: #e2e2e2 } - .terminal-1144763792-r15 { fill: #e2e2e2;text-decoration: underline; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▎▊ - ▎Welcome to the nf-core pipeline creation wizard▊ - ▎▊ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline  - template. - - The template helps anyone benefit from nf-core best practices, and is a requirement for  - nf-core pipelines. - - ▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans  - ▌with the community as early as possible; ideally before you start on your pipeline! See  - ▌the nf-core guidelines and the #new-pipelines Slack channel for more information. - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go! - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - -  D  Toggle dark mode  Q  Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + +                                           ,--./,-. +           ___     __   __   __   ___     /,-._.--~\  +     |\ | |__  __ /  ` /  \ |__) |__         }  { +     | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                           `._,._,' + + + + Welcome to the nf-core pipeline creation wizard + + This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + + The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core  + pipelines. + + ▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with + ▌the community as early as possible; ideally before you start on your pipeline! See the  + ▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go! + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit From d77af41897561d70b99efbda87a223c7c05cf816 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 23 May 2024 11:07:10 +0000 Subject: [PATCH 16/26] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c1b3a97663..16262bd1c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ - Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) +- update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 8f6c8fb5ff34eecf2f9b0c502753de77123641b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 23 May 2024 11:21:49 +0000 Subject: [PATCH 17/26] update snapshots fom gitpod --- tests/__snapshots__/test_create_app.ambr | 266 +++++++++--------- .../pytest-0/test_github_details0 | 1 + .../pytest-0/test_github_exit_message0 | 1 + .../pytest-0/test_github_question0 | 1 + 4 files changed, 135 insertions(+), 134 deletions(-) create mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_details0 create mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 create mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_question0 diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index f5a519b133..ed7bf8b256 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -1408,262 +1408,260 @@ font-weight: 700; } - .terminal-1242773313-matrix { + .terminal-3893066652-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1242773313-title { + .terminal-3893066652-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1242773313-r1 { fill: #c5c8c6 } - .terminal-1242773313-r2 { fill: #e3e3e3 } - .terminal-1242773313-r3 { fill: #989898 } - .terminal-1242773313-r4 { fill: #e1e1e1 } - .terminal-1242773313-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1242773313-r6 { fill: #18954b } - .terminal-1242773313-r7 { fill: #e2e2e2 } - .terminal-1242773313-r8 { fill: #e2e2e2;font-style: italic; } - .terminal-1242773313-r9 { fill: #e2e2e2;font-style: italic;;text-decoration: underline; } - .terminal-1242773313-r10 { fill: #a5a5a5;font-style: italic; } - .terminal-1242773313-r11 { fill: #1e1e1e } - .terminal-1242773313-r12 { fill: #008139 } - .terminal-1242773313-r13 { fill: #454a50 } - .terminal-1242773313-r14 { fill: #787878 } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - ▌💡 Found GitHub username in local GitHub CLI config - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ + ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + +  d Toggle dark mode q Quit diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 new file mode 160000 index 0000000000..19fc648c4a --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 @@ -0,0 +1 @@ +Subproject commit 19fc648c4a1fc31b474b13cbfebd322ce9538b95 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 new file mode 160000 index 0000000000..75465e6bd7 --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 @@ -0,0 +1 @@ +Subproject commit 75465e6bd715b1bf9075c7efbce1f2dd38c4df37 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 new file mode 160000 index 0000000000..07281e3aa6 --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 @@ -0,0 +1 @@ +Subproject commit 07281e3aa6aef6d8a282c1cafaf7defaef745565 From e9740b6454df2b238fd2c7a1ab407eee9b193029 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 23 May 2024 12:03:25 +0000 Subject: [PATCH 18/26] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.5 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4b1941d81e..01bd13a9e9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.4 + rev: v0.4.5 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From e7136379bbadd7d3c883a9c80be3d37ce68a307c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 27 May 2024 13:06:23 +0200 Subject: [PATCH 19/26] return directory if base_dir is the root directory --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 8c50f0a49f..1a1e8a2a99 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1069,7 +1069,7 @@ def determine_base_dir(directory="."): config_fn = get_first_available_path(base_dir, CONFIG_PATHS) if config_fn: break - return directory if base_dir == start_dir else base_dir + return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir def get_first_available_path(directory, paths): From ae47db3608feaa95cb9165a876740fcee96534ac Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 27 May 2024 11:07:57 +0000 Subject: [PATCH 20/26] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16262bd1c3..a5795245a2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) +- return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From efd397d94ee223f8dd60f1c3a88a04211bc4b27e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 27 May 2024 14:39:17 +0200 Subject: [PATCH 21/26] add org to main.nf.test tag --- nf_core/components/create.py | 4 ++++ nf_core/module-template/tests/main.nf.test.j2 | 2 +- nf_core/subworkflow-template/tests/main.nf.test.j2 | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 6c9c01b496..e603db3857 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -157,6 +157,10 @@ def create(self): if self.component_type == "modules": self._get_module_structure_components() + # Add a valid organization name for nf-test tags + not_alphabet = re.compile(r'[^a-zA-Z]') + self.org_alphabet = not_alphabet.sub('', self.org) + # Create component template with jinja2 self._render_template() log.info(f"Created component template: '{self.component_name}'") diff --git a/nf_core/module-template/tests/main.nf.test.j2 b/nf_core/module-template/tests/main.nf.test.j2 index 1f70df64b0..456c989f85 100644 --- a/nf_core/module-template/tests/main.nf.test.j2 +++ b/nf_core/module-template/tests/main.nf.test.j2 @@ -7,7 +7,7 @@ nextflow_process { process "{{ component_name_underscore|upper }}" tag "modules" - tag "modules_nfcore" + tag "modules_{{ org_alphabet }}" {%- if subtool %} tag "{{ component }}" {%- endif %} diff --git a/nf_core/subworkflow-template/tests/main.nf.test.j2 b/nf_core/subworkflow-template/tests/main.nf.test.j2 index c44e19a4e4..8aaf6e0c7c 100644 --- a/nf_core/subworkflow-template/tests/main.nf.test.j2 +++ b/nf_core/subworkflow-template/tests/main.nf.test.j2 @@ -7,7 +7,7 @@ nextflow_workflow { workflow "{{ component_name_underscore|upper }}" tag "subworkflows" - tag "subworkflows_nfcore" + tag "subworkflows_{{ org_alphabet }}" tag "subworkflows/{{ component_name }}" // TODO nf-core: Add tags for all modules used within this subworkflow. Example: tag "samtools" From a446f29d01470e05870552d6bb496236460d46b6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 27 May 2024 15:19:50 +0200 Subject: [PATCH 22/26] make sure linting passes this new feature --- nf_core/modules/lint/module_tests.py | 6 +++++- nf_core/subworkflows/lint/subworkflow_tests.py | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index b2b6c2221f..080fc2bdc8 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -4,6 +4,7 @@ import json import logging +import re from pathlib import Path import yaml @@ -137,7 +138,10 @@ def module_tests(_, module: NFCoreComponent): ) # Verify that tags are correct. main_nf_tags = module._get_main_nf_tags(module.nftest_main_nf) - required_tags = ["modules", "modules_nfcore", module.component_name] + not_alphabet = re.compile(r'[^a-zA-Z]') + org_alp = not_alphabet.sub('', module.org) + org_alphabet = org_alp if org_alp != "" else "nfcore" + required_tags = ["modules", f"modules_{org_alphabet}", module.component_name] if module.component_name.count("/") == 1: required_tags.append(module.component_name.split("/")[0]) chained_components_tags = module._get_included_components_in_chained_tests(module.nftest_main_nf) diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index cfae2d553c..87e850e8fb 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -4,6 +4,7 @@ import json import logging +import re from pathlib import Path import yaml @@ -144,10 +145,13 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): ) # Verify that tags are correct. main_nf_tags = subworkflow._get_main_nf_tags(subworkflow.nftest_main_nf) + not_alphabet = re.compile(r'[^a-zA-Z]') + org_alp = not_alphabet.sub('', subworkflow.org) + org_alphabet = org_alp if org_alp != "" else "nfcore" required_tags = [ "subworkflows", f"subworkflows/{subworkflow.component_name}", - "subworkflows_nfcore", + f"subworkflows_{org_alphabet}", ] included_components = [] if subworkflow.main_nf.is_file(): From 7bae122e1da8fb54511ebdfe02894a602621dbce Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 27 May 2024 15:27:20 +0200 Subject: [PATCH 23/26] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16262bd1c3..259982e39f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### Components +- The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) + ### General - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974)) From a4ecb70909da3b6986c25d8986ba956391bcd0fc Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 27 May 2024 15:32:45 +0200 Subject: [PATCH 24/26] ruff! --- nf_core/components/create.py | 4 ++-- nf_core/modules/lint/module_tests.py | 4 ++-- nf_core/subworkflows/lint/subworkflow_tests.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/nf_core/components/create.py b/nf_core/components/create.py index e603db3857..78c30b5179 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -158,8 +158,8 @@ def create(self): self._get_module_structure_components() # Add a valid organization name for nf-test tags - not_alphabet = re.compile(r'[^a-zA-Z]') - self.org_alphabet = not_alphabet.sub('', self.org) + not_alphabet = re.compile(r"[^a-zA-Z]") + self.org_alphabet = not_alphabet.sub("", self.org) # Create component template with jinja2 self._render_template() diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 080fc2bdc8..4bf4ea7745 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -138,8 +138,8 @@ def module_tests(_, module: NFCoreComponent): ) # Verify that tags are correct. main_nf_tags = module._get_main_nf_tags(module.nftest_main_nf) - not_alphabet = re.compile(r'[^a-zA-Z]') - org_alp = not_alphabet.sub('', module.org) + not_alphabet = re.compile(r"[^a-zA-Z]") + org_alp = not_alphabet.sub("", module.org) org_alphabet = org_alp if org_alp != "" else "nfcore" required_tags = ["modules", f"modules_{org_alphabet}", module.component_name] if module.component_name.count("/") == 1: diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index 87e850e8fb..fe7b40407a 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -145,8 +145,8 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): ) # Verify that tags are correct. main_nf_tags = subworkflow._get_main_nf_tags(subworkflow.nftest_main_nf) - not_alphabet = re.compile(r'[^a-zA-Z]') - org_alp = not_alphabet.sub('', subworkflow.org) + not_alphabet = re.compile(r"[^a-zA-Z]") + org_alp = not_alphabet.sub("", subworkflow.org) org_alphabet = org_alp if org_alp != "" else "nfcore" required_tags = [ "subworkflows", From 6d9feb3a900db74980bce66523e65f2470cdb507 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 28 May 2024 22:45:25 +0000 Subject: [PATCH 25/26] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 01bd13a9e9..8521c44100 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.5 + rev: v0.4.6 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From f94ec87ccd246eba4db29609e1b0f5ed44b2fb80 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 28 May 2024 22:46:12 +0000 Subject: [PATCH 26/26] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ae43fd4e7b..63bef50b84 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]