From f2b282c696ebfff78ac4e328dca3d9a25b258ec4 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 21 Aug 2024 16:12:58 +0200 Subject: [PATCH 1/7] add option to exclude fastqc from pipeline template --- nf_core/pipeline-template/CITATIONS.md | 7 +++---- nf_core/pipeline-template/README.md | 4 ++-- nf_core/pipeline-template/conf/modules.config | 2 ++ nf_core/pipeline-template/docs/output.md | 9 ++++++--- nf_core/pipeline-template/modules.json | 3 ++- .../local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++-- nf_core/pipeline-template/workflows/pipeline.nf | 4 +++- nf_core/pipelines/create/templatefeatures.yml | 10 ++++++++++ 8 files changed, 30 insertions(+), 13 deletions(-) diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 7cf37e5018..2373f1de7f 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -12,11 +12,10 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +{% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - -{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. > {%- endif %} diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 7718d2e5f8..a618f87bf7 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -44,8 +44,8 @@ workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. --> -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) - {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %} +{% if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %} +{% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %} ## Usage diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config index 84972d8e24..078142fad0 100644 --- a/nf_core/pipeline-template/conf/modules.config +++ b/nf_core/pipeline-template/conf/modules.config @@ -18,9 +18,11 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + {%- if fastqc %} withName: FASTQC { ext.args = '--quiet' } + {%- endif %} {%- if multiqc %} withName: 'MULTIQC' { diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 76195a6825..5e42d50cc5 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -12,10 +12,13 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC - {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %} +{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %} +{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %} + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +{%- if fastqc %} + ### FastQC
@@ -28,7 +31,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - +{%- endif %} {%- if multiqc %} ### MultiQC diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 8b156083f3..6ab68d0f2a 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -5,11 +5,12 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + {%- if fastqc %} "fastqc": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] - }{%- if multiqc %}, + }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 3db8f66cb6..fe9e558cfe 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -230,7 +230,7 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", + {% if fastqc %}"FastQC (Andrews 2010),",{% endif %} "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -243,7 +243,7 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + {% if fastqc %}"
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ",{% endif %} "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index d98c392f0c..e15d32f977 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { FASTQC } from '../modules/nf-core/fastqc/main' +{% if fastqc %}include { FASTQC } from '../modules/nf-core/fastqc/main'{% endif %} {% if multiqc %}include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endif %} include { paramsSummaryMap } from 'plugin/nf-validation' {% if multiqc %}include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %} @@ -27,6 +27,7 @@ workflow {{ short_name|upper }} { ch_versions = Channel.empty() {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %} + {%- if fastqc %} // // MODULE: Run FastQC // @@ -35,6 +36,7 @@ workflow {{ short_name|upper }} { ) {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %} ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + {%- endif %} // // Collate and save software versions diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 6a5fac358d..9fb56d610f 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -228,6 +228,16 @@ multiqc: multiqc_config: False nfcore_pipelines: True custom_pipelines: True +fastqc: + skippable_paths: + - "modules/nf-core/fastqc/" + short_description: "Use fastqc" + description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." + help_text: | + FastQC is a tool which provides quality control checks on raw sequencing data. + The pipeline will include the FastQC module. + nfcore_pipelines: True + custom_pipelines: True changelog: skippable_paths: - "CHANGELOG.md" From e4f685d90e48c9ba0d01312eeae4fb2238afb000 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 21 Aug 2024 14:34:56 +0000 Subject: [PATCH 2/7] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1527f5ba49..6415612bbf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) +- add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129)) ### Linting From 0e4a7d1393fbe944f39e6c38219c43d02831999a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 11:31:14 +0200 Subject: [PATCH 3/7] don't fail when no nf-core modules installed --- nf_core/components/lint/__init__.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index d0f6685365..0373170cfb 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -114,9 +114,7 @@ def __init__( ) ) if not self.all_remote_components: - raise LookupError( - f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." - ) + log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") local_component_dir = Path(self.directory, self.component_type, "local") if local_component_dir.exists(): @@ -146,7 +144,7 @@ def __init__( ] self.all_local_components = [] if not self.all_remote_components: - raise LookupError(f"No {self.component_type} in '{self.component_type}' directory") + log.debug(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) From 92618ad8be8362ba5bece5eb82ab44fc08012c21 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 11:46:39 +0200 Subject: [PATCH 4/7] fix versions yaml file name --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index e15d32f977..8c797ede38 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -44,7 +44,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From d437582e632ad7bed1768a684eafdeba13cd16cf Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 12:46:28 +0200 Subject: [PATCH 5/7] udpate bpipe and fix pytests --- nf_core/components/lint/__init__.py | 4 ++-- nf_core/modules/lint/__init__.py | 2 +- tests/modules/test_lint.py | 11 +++++------ tests/subworkflows/test_lint.py | 10 ++++------ tests/test_modules.py | 4 ++-- 5 files changed, 14 insertions(+), 17 deletions(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 0373170cfb..c1b1f24cb7 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -114,7 +114,7 @@ def __init__( ) ) if not self.all_remote_components: - log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") + log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") local_component_dir = Path(self.directory, self.component_type, "local") if local_component_dir.exists(): @@ -144,7 +144,7 @@ def __init__( ] self.all_local_components = [] if not self.all_remote_components: - log.debug(f"No {self.component_type} in '{self.component_type}' directory") + log.warning(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index b75f7e7570..017b3965b4 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -110,7 +110,7 @@ def lint( """ # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class # Prompt for module or all - if module is None and not all_modules: + if module is None and not all_modules and len(self.all_remote_components) > 0: questions = [ { "type": "list", diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index dfe288a6ee..cc7e0565e0 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -2,7 +2,6 @@ from pathlib import Path from typing import Union -import pytest import yaml from git.repo import Repo @@ -191,8 +190,8 @@ def test_modules_lint_empty(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text def test_modules_lint_new_modules(self): """lint a new module""" @@ -206,8 +205,8 @@ def test_modules_lint_no_gitlab(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text def test_modules_lint_gitlab_modules(self): """Lint modules from a different remote""" @@ -566,7 +565,7 @@ def test_modules_meta_yml_input_mismatch(self): fh.write(main_nf) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2 + assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}" lint_tests = [x.lint_test for x in module_lint.warned] # check that it is there twice: assert lint_tests.count("meta_input_meta_only") == 1 diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py index 2693008707..c8b97fd0b0 100644 --- a/tests/subworkflows/test_lint.py +++ b/tests/subworkflows/test_lint.py @@ -2,8 +2,6 @@ import shutil from pathlib import Path -import pytest - import nf_core.subworkflows from ..test_subworkflows import TestSubworkflows @@ -25,8 +23,8 @@ def test_subworkflows_lint_empty(self): self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True) self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True) self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True) - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) + assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text def test_subworkflows_lint_new_subworkflow(self): """lint a new subworkflow""" @@ -39,8 +37,8 @@ def test_subworkflows_lint_new_subworkflow(self): def test_subworkflows_lint_no_gitlab(self): """Test linting a pipeline with no subworkflows installed""" - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No subworkflows from {GITLAB_URL} installed in pipeline" in self.caplog.text def test_subworkflows_lint_gitlab_subworkflows(self): """Lint subworkflows from a different remote""" diff --git a/tests/test_modules.py b/tests/test_modules.py index 9ce74fd4e1..0e16497176 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -44,8 +44,8 @@ def create_modules_repo_dummy(tmp_dir): yaml.dump(nf_core_yml.model_dump(), fh) # mock biocontainers and anaconda response with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") - mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") + mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") + mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules module_create = nf_core.modules.create.ModuleCreate( root_dir, "bpipe/test", "@author", "process_single", False, False From 9551cdc3467dca4b4cd1bc3d3bf735340b9ee7bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 26 Aug 2024 14:21:37 +0200 Subject: [PATCH 6/7] 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 --- nf_core/pipeline-template/conf/modules.config | 2 +- .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config index 078142fad0..35e861d9b1 100644 --- a/nf_core/pipeline-template/conf/modules.config +++ b/nf_core/pipeline-template/conf/modules.config @@ -18,7 +18,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - {%- if fastqc %} + {% if fastqc -%} withName: FASTQC { ext.args = '--quiet' } diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index fe9e558cfe..b130b7f88a 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -231,7 +231,7 @@ def toolCitationText() { def citation_text = [ "Tools used in the workflow included:", {% if fastqc %}"FastQC (Andrews 2010),",{% endif %} - "MultiQC (Ewels et al. 2016)", + {% if multiqc %}"MultiQC (Ewels et al. 2016)",{% endif %} "." ].join(' ').trim() @@ -244,7 +244,7 @@ def toolBibliographyText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ {% if fastqc %}"
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ",{% endif %} - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + {% if multiqc %}"
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • "{% endif %} ].join(' ').trim() return reference_text From 9d29e9342b5258b8c08f495d49409761707493c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 26 Aug 2024 12:25:34 +0000 Subject: [PATCH 7/7] update textual snapshots --- .../__snapshots__/test_create_app.ambr | 764 +++++++++--------- .../pytest-0/test_github_details0 | 1 - .../pytest-0/test_github_exit_message0 | 1 - .../pytest-0/test_github_question0 | 1 - .../pytest-1/test_github_details0 | 1 - .../pytest-1/test_github_exit_message0 | 1 - .../pytest-1/test_github_question0 | 1 - 7 files changed, 382 insertions(+), 388 deletions(-) delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_details0 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_question0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_details0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_question0 diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index ee470c915c..f5a19837b6 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-3293903238-matrix { + .terminal-1136262003-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3293903238-title { + .terminal-1136262003-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3293903238-r1 { fill: #c5c8c6 } - .terminal-3293903238-r2 { fill: #e3e3e3 } - .terminal-3293903238-r3 { fill: #989898 } - .terminal-3293903238-r4 { fill: #e1e1e1 } - .terminal-3293903238-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3293903238-r6 { fill: #1e1e1e } - .terminal-3293903238-r7 { fill: #507bb3 } - .terminal-3293903238-r8 { fill: #e2e2e2 } - .terminal-3293903238-r9 { fill: #808080 } - .terminal-3293903238-r10 { fill: #dde6ed;font-weight: bold } - .terminal-3293903238-r11 { fill: #001541 } - .terminal-3293903238-r12 { fill: #0178d4 } - .terminal-3293903238-r13 { fill: #454a50 } - .terminal-3293903238-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-3293903238-r15 { fill: #000000 } - .terminal-3293903238-r16 { fill: #14191f } - .terminal-3293903238-r17 { fill: #e4e4e4 } - .terminal-3293903238-r18 { fill: #7ae998 } - .terminal-3293903238-r19 { fill: #0a180e;font-weight: bold } - .terminal-3293903238-r20 { fill: #008139 } - .terminal-3293903238-r21 { fill: #fea62b;font-weight: bold } - .terminal-3293903238-r22 { fill: #a7a9ab } - .terminal-3293903238-r23 { fill: #e2e3e3 } + .terminal-1136262003-r1 { fill: #c5c8c6 } + .terminal-1136262003-r2 { fill: #e3e3e3 } + .terminal-1136262003-r3 { fill: #989898 } + .terminal-1136262003-r4 { fill: #e1e1e1 } + .terminal-1136262003-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1136262003-r6 { fill: #1e1e1e } + .terminal-1136262003-r7 { fill: #507bb3 } + .terminal-1136262003-r8 { fill: #e2e2e2 } + .terminal-1136262003-r9 { fill: #808080 } + .terminal-1136262003-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1136262003-r11 { fill: #001541 } + .terminal-1136262003-r12 { fill: #0178d4 } + .terminal-1136262003-r13 { fill: #454a50 } + .terminal-1136262003-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-1136262003-r15 { fill: #000000 } + .terminal-1136262003-r16 { fill: #14191f } + .terminal-1136262003-r17 { fill: #e4e4e4 } + .terminal-1136262003-r18 { fill: #7ae998 } + .terminal-1136262003-r19 { fill: #0a180e;font-weight: bold } + .terminal-1136262003-r20 { fill: #008139 } + .terminal-1136262003-r21 { fill: #fea62b;font-weight: bold } + .terminal-1136262003-r22 { fill: #a7a9ab } + .terminal-1136262003-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎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. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎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. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-2443134963-matrix { + .terminal-242174438-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2443134963-title { + .terminal-242174438-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2443134963-r1 { fill: #c5c8c6 } - .terminal-2443134963-r2 { fill: #e3e3e3 } - .terminal-2443134963-r3 { fill: #989898 } - .terminal-2443134963-r4 { fill: #e1e1e1 } - .terminal-2443134963-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2443134963-r6 { fill: #1e1e1e } - .terminal-2443134963-r7 { fill: #507bb3 } - .terminal-2443134963-r8 { fill: #e2e2e2 } - .terminal-2443134963-r9 { fill: #808080 } - .terminal-2443134963-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2443134963-r11 { fill: #001541 } - .terminal-2443134963-r12 { fill: #14191f } - .terminal-2443134963-r13 { fill: #454a50 } - .terminal-2443134963-r14 { fill: #7ae998 } - .terminal-2443134963-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-2443134963-r16 { fill: #0a180e;font-weight: bold } - .terminal-2443134963-r17 { fill: #000000 } - .terminal-2443134963-r18 { fill: #008139 } - .terminal-2443134963-r19 { fill: #fea62b;font-weight: bold } - .terminal-2443134963-r20 { fill: #a7a9ab } - .terminal-2443134963-r21 { fill: #e2e3e3 } + .terminal-242174438-r1 { fill: #c5c8c6 } + .terminal-242174438-r2 { fill: #e3e3e3 } + .terminal-242174438-r3 { fill: #989898 } + .terminal-242174438-r4 { fill: #e1e1e1 } + .terminal-242174438-r5 { fill: #4ebf71;font-weight: bold } + .terminal-242174438-r6 { fill: #1e1e1e } + .terminal-242174438-r7 { fill: #507bb3 } + .terminal-242174438-r8 { fill: #e2e2e2 } + .terminal-242174438-r9 { fill: #808080 } + .terminal-242174438-r10 { fill: #dde6ed;font-weight: bold } + .terminal-242174438-r11 { fill: #001541 } + .terminal-242174438-r12 { fill: #14191f } + .terminal-242174438-r13 { fill: #454a50 } + .terminal-242174438-r14 { fill: #7ae998 } + .terminal-242174438-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-242174438-r16 { fill: #0a180e;font-weight: bold } + .terminal-242174438-r17 { fill: #000000 } + .terminal-242174438-r18 { fill: #008139 } + .terminal-242174438-r19 { fill: #fea62b;font-weight: bold } + .terminal-242174438-r20 { fill: #a7a9ab } + .terminal-242174438-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help ▃▃ - ▊▁▁▁▁▁▁▁▁▎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 - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▆▆ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎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 + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2511,254 +2511,254 @@ 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 - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most common - reference genome files  - from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use multiqcThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - module which generates  - an HTML report for  - quality control. - - - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most common + reference genome files  + from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use multiqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which generates  + an HTML report for  + quality control. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use fastqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which performs  + quality control  + analysis of input FASTQ + files. + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  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 deleted file mode 160000 index ee82f320cb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 deleted file mode 160000 index f7fe48cf9d..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 deleted file mode 160000 index dce3324acb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit dce3324acbbe32f905afae8553e042f39404b37e diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0 deleted file mode 160000 index e2638dca91..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 deleted file mode 160000 index 74cda800a8..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0 deleted file mode 160000 index 444ebc5370..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045