eager
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Published
20 hours ago •
nf-core
nf-core
Fixed TSV input documentation
Removed the second fastq in the SE data in the example of the TSV input, since this should be NA for single-end data
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nf-core lint .). - [ ] Ensure the test suite passes (
nextflow run . -profile test,docker). - [x] Usage Documentation in
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docs/output.mdis updated. - [ ]
CHANGELOG.mdis updated. - [ ]
README.mdis updated (including new tool citations and authors/contributors).
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basetodev - This CI test will remain failed until you push a new commit
Hi @aidaanva,
It looks like this pull-request is has been made against the nf-core/eager master branch.
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Thanks again for your contribution!
![github-actions[bot] avatar](https://avatars.githubusercontent.com/in/15368?v=4 "Published by a pub.dev verified publisher"){kind=small}
nf-core lint overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit 8b42000
+| ✅ 388 tests passed |+
#| ❔ 5 tests were ignored |#
!| ❗ 30 tests had warnings |!
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params_used - Config variable found in
main.nf:params.hostnames -
params_used - Config variable found in
main.nf:params.config_profile_description -
params_used - Config variable found in
main.nf:params.config_profile_contact -
params_used - Config variable found in
main.nf:params.config_profile_url -
params_used - Config variable found in
main.nf:params.max_memory -
params_used - Config variable found in
main.nf:params.max_cpus -
params_used - Config variable found in
main.nf:params.max_time -
files_unchanged -
.gitattributesmatches the template -
files_unchanged -
CODE_OF_CONDUCT.mdmatches the template -
files_unchanged -
LICENSEmatches the template -
files_unchanged -
.github/.dockstore.ymlmatches the template -
files_unchanged -
.github/ISSUE_TEMPLATE/config.ymlmatches the template -
files_unchanged -
.github/ISSUE_TEMPLATE/feature_request.mdmatches the template -
files_unchanged -
.github/markdownlint.ymlmatches the template -
files_unchanged -
.github/PULL_REQUEST_TEMPLATE.mdmatches the template -
files_unchanged -
.github/workflows/branch.ymlmatches the template -
files_unchanged -
.github/workflows/linting_comment.ymlmatches the template -
files_unchanged -
assets/email_template.htmlmatches the template -
files_unchanged -
assets/email_template.txtmatches the template -
files_unchanged -
assets/sendmail_template.txtmatches the template -
files_unchanged -
assets/nf-core-eager_logo.pngmatches the template -
files_unchanged -
bin/markdown_to_html.pymatches the template -
files_unchanged -
docs/images/nf-core-eager_logo.pngmatches the template -
files_unchanged -
lib/nfcore_external_java_deps.jarmatches the template -
files_unchanged -
lib/NfcoreSchema.groovymatches the template -
files_unchanged -
.gitignorematches the template -
files_unchanged -
.github/workflows/push_dockerhub_dev.ymlmatches the template -
files_unchanged -
.github/workflows/push_dockerhub_release.ymlmatches the template - actions_ci - '.github/workflows/ci.yml' is triggered on expected events
-
actions_ci - CI is building the correct docker image:
docker build --no-cache . -t nfcore/eager:dev - actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
- actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
- actions_ci - '.github/workflows/ci.yml' checks minimum NF version
- actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
-
actions_awsfulltest -
.github/workflows/awsfulltest.ymlis triggered correctly -
actions_awsfulltest -
.github/workflows/awsfulltest.ymldoes not use-profile test -
readme - README Nextflow minimum version badge matched config. Badge:
20.07.1, Config:20.07.1 - readme - README had a bioconda badge
- conda_env_yaml - Conda environment name was correct (nf-core-eager-2.4.5dev)
-
conda_env_yaml - Conda dep had pinned version number:
conda-forge::python=3.9.4 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::markdown=3.3.4 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::pymdown-extensions=8.2 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::pygments=2.9.0 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::rename=1.601 -
conda_env_yaml - Conda package is the latest available:
bioconda::rename=1.601 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::openjdk=8.0.144 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::fastqc=0.11.9 -
conda_env_yaml - Conda package is the latest available:
bioconda::fastqc=0.11.9 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::adapterremoval=2.3.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::adapterremovalfixprefix=0.0.5 -
conda_env_yaml - Conda package is the latest available:
bioconda::adapterremovalfixprefix=0.0.5 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bwa=0.7.17 -
conda_env_yaml - Conda package is the latest available:
bioconda::bwa=0.7.17 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::picard=2.26.0 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::samtools=1.12 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::dedup=0.12.8 -
conda_env_yaml - Conda package is the latest available:
bioconda::dedup=0.12.8 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::angsd=0.935 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::circularmapper=1.93.5 -
conda_env_yaml - Conda package is the latest available:
bioconda::circularmapper=1.93.5 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::gatk4=4.2.0.0 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::gatk=3.5 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::qualimap=2.2.2d -
conda_env_yaml - Conda package is the latest available:
bioconda::qualimap=2.2.2d -
conda_env_yaml - Conda dep had pinned version number:
bioconda::vcf2genome=0.91 -
conda_env_yaml - Conda package is the latest available:
bioconda::vcf2genome=0.91 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::damageprofiler=0.4.9 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::multiqc=1.13a -
conda_env_yaml - Conda package is the latest available:
bioconda::multiqc=1.13a -
conda_env_yaml - Conda dep had pinned version number:
bioconda::pmdtools=0.60 -
conda_env_yaml - Conda package is the latest available:
bioconda::pmdtools=0.60 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bedtools=2.30.0 -
conda_env_yaml - Conda package is the latest available:
bioconda::bedtools=2.30.0 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::libiconv=1.16 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::pigz=2.6 -
conda_env_yaml - Conda package is the latest available:
conda-forge::pigz=2.6 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::sequencetools=1.5.2 -
conda_env_yaml - Conda package is the latest available:
bioconda::sequencetools=1.5.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::preseq=3.1.2 -
conda_env_yaml - Conda package is the latest available:
bioconda::preseq=3.1.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::fastp=0.20.1 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bamutil=1.0.15 -
conda_env_yaml - Conda package is the latest available:
bioconda::bamutil=1.0.15 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::mtnucratio=0.7 -
conda_env_yaml - Conda package is the latest available:
bioconda::mtnucratio=0.7 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::pysam=0.16.0 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::kraken2=2.1.2 -
conda_env_yaml - Conda package is the latest available:
bioconda::kraken2=2.1.2 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::pandas=1.2.4 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::freebayes=1.3.5 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::sexdeterrmine=1.1.2 -
conda_env_yaml - Conda package is the latest available:
bioconda::sexdeterrmine=1.1.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::multivcfanalyzer=0.85.2 -
conda_env_yaml - Conda package is the latest available:
bioconda::multivcfanalyzer=0.85.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::hops=0.35 -
conda_env_yaml - Conda package is the latest available:
bioconda::hops=0.35 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::biopython=1.79 -
conda_env_yaml - Conda package is the latest available:
conda-forge::biopython=1.79 -
conda_env_yaml - Conda dep had pinned version number:
conda-forge::xopen=1.1.0 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bowtie2=2.4.4 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::eigenstratdatabasetools=1.0.2 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::mapdamage2=2.2.1 -
conda_env_yaml - Conda package is the latest available:
bioconda::mapdamage2=2.2.1 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bbmap=38.92 -
conda_env_yaml - Conda dep had pinned version number:
bioconda::bcftools=1.12 - conda_dockerfile - Found all expected strings in Dockerfile file
- pipeline_name_conventions - Name adheres to nf-core convention
- template_strings - Did not find any Jinja template strings (151 files)
- schema_lint - Schema lint passed
- schema_lint - Schema title + description lint passed
- schema_params - Schema matched params returned from nextflow config
- actions_schema_validation - Workflow validation passed: linting.yml
- actions_schema_validation - Workflow validation passed: awsfulltest.yml
- actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
- actions_schema_validation - Workflow validation passed: branch.yml
- actions_schema_validation - Workflow validation passed: awstest.yml
- actions_schema_validation - Workflow validation passed: linting_comment.yml
- actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
- actions_schema_validation - Workflow validation passed: ci.yml
- merge_markers - No merge markers found in pipeline files
Run details
- nf-core/tools version 1.14
- Run at
2022-08-25 13:18:18