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A basic workflow now running successfully
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GallVp committed Feb 20, 2024
1 parent 24151a6 commit 8198830
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100 changes: 50 additions & 50 deletions .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,53 +2,53 @@ name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used
to launch the pipeline and the output from your terminal.
render: console
placeholder: '$ nextflow run ...
Some output where something broke
'
- type: textarea
id: files
attributes:
label: Relevant files
description: 'Please drag and drop the relevant files here. Create a `.zip` archive
if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
in the directory where you launched the pipeline)_ as well as custom Nextflow
configuration files.
'
- type: textarea
id: system
attributes:
label: System information
description: '* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of plant-food-research-open/assemblyqc _(eg. 1.1, 1.5, 1.8.2)_
'
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used
to launch the pipeline and the output from your terminal.
render: console
placeholder: "$ nextflow run ...
Some output where something broke
"
- type: textarea
id: files
attributes:
label: Relevant files
description: "Please drag and drop the relevant files here. Create a `.zip` archive
if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
in the directory where you launched the pipeline)_ as well as custom Nextflow
configuration files.
"
- type: textarea
id: system
attributes:
label: System information
description: "* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of plant-food-research-open/assemblyqc _(eg. 1.1, 1.5, 1.8.2)_
"
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "22.04.3"
- "latest-everything"
steps:
- name: Check out pipeline code
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2 changes: 1 addition & 1 deletion .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
Expand Up @@ -64,4 +64,4 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
30 changes: 15 additions & 15 deletions .nf-core.yml
Original file line number Diff line number Diff line change
@@ -1,23 +1,23 @@
lint:
files_exist:
- CODE_OF_CONDUCT.md
- assets/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- CODE_OF_CONDUCT.md
- assets/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
files_unchanged:
- CODE_OF_CONDUCT.md
- assets/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_dark.png
- .github/ISSUE_TEMPLATE/bug_report.yml
- CODE_OF_CONDUCT.md
- assets/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_light.png
- docs/images/nf-core-assemblyqc_logo_dark.png
- .github/ISSUE_TEMPLATE/bug_report.yml
multiqc_config:
- report_comment
- report_comment
nextflow_config:
- manifest.name
- manifest.homePage
- manifest.name
- manifest.homePage
repository_type: pipeline
template:
prefix: plant-food-research-open
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v3.1.1"
rev: "v3.1.0"
hooks:
- id: prettier
- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[![GitHub Actions CI Status](https://github.com/plant-food-research-open/assemblyqc/workflows/nf-core%20CI/badge.svg)](https://github.com/plant-food-research-open/assemblyqc/actions?query=workflow%3A%22nf-core+CI%22)
[![GitHub Actions Linting Status](https://github.com/plant-food-research-open/assemblyqc/workflows/nf-core%20linting/badge.svg)](https://github.com/plant-food-research-open/assemblyqc/actions?query=workflow%3A%22nf-core+linting%22)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.3-23aa62.svg)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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2 changes: 2 additions & 0 deletions assets/assemblysheet.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
tag,fasta,gff3,monoploid_ids,hic_reads,synteny_labels
FI1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.fna.gz,,,,
3 changes: 0 additions & 3 deletions assets/samplesheet.csv

This file was deleted.

59 changes: 49 additions & 10 deletions assets/schema_input.json
Original file line number Diff line number Diff line change
Expand Up @@ -7,22 +7,61 @@
"items": {
"type": "object",
"properties": {
"sample": {
"tag": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces"
"pattern": "^\\w+$",
"errorMessage": "Assembly tags must be provided and can only contain alphanumeric characters including '_'"
},
"fastq_1": {
"fasta": {
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"pattern": "^\\S+\\.f(ast|as|sa|na)?\\.gz$",
"errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(ast|as|sa|na)' or '.f(ast|as|sa|na).gz'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"gff3": {
"type": "string",
"pattern": "^\\S+\\.gff(3)?\\.gz$",
"errorMessage": "GFF3 file path cannot contain spaces and must have extension '.gff.gz' or '.gff3.gz'"
},
"monoploid_ids": {
"errorMessage": "Monoploid IDs txt file path cannot contain spaces and must have extension '.txt'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.txt$"
},
{
"type": "string",
"maxLength": 0
}
]
},
"hic_reads": {
"errorMessage": "HiC reads should either be provided as a SRA ID or as a path to paired reads with pattern '*_R{1,2}.(fastq|fq).gz'",
"anyOf": [
{
"type": "string",
"pattern": "^SR\\w+$"
},
{
"type": "string",
"pattern": "^\\S+_R\\{1,2\\}\\.f(ast)?q\\.gz$"
},
{
"type": "string",
"maxLength": 0
}
]
},
"synteny_labels": {
"errorMessage": "Synteny labels tsv path cannot contain spaces and must have extension '.tsv'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
"pattern": "^SR\\w+$"
},
{
"type": "string",
"pattern": "^\\S+_R\\{1,2\\}\\.f(ast)?q\\.gz$"
},
{
"type": "string",
Expand All @@ -31,6 +70,6 @@
]
}
},
"required": ["sample", "fastq_1"]
"required": ["tag", "fasta"]
}
}
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