From e6e67c3e72e7294c521c06fd8138fc75fccf282c Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 23 Mar 2022 13:48:13 +0000
Subject: [PATCH] Template update for nf-core/tools version 2.3.1
---
.editorconfig | 5 +-
.github/CONTRIBUTING.md | 15 +-
.github/ISSUE_TEMPLATE/bug_report.yml | 1 -
.github/PULL_REQUEST_TEMPLATE.md | 6 +-
.github/workflows/awsfulltest.yml | 1 -
.github/workflows/awstest.yml | 2 +-
.github/workflows/branch.yml | 5 +-
.github/workflows/ci.yml | 12 +-
.github/workflows/linting.yml | 85 ++---------
.github/workflows/linting_comment.yml | 3 +-
.gitpod.yml | 16 +-
.markdownlint.yml | 14 --
.prettierrc.yml | 1 +
.yamllint.yml | 6 -
CHANGELOG.md | 2 +
CITATIONS.md | 27 ++--
README.md | 31 ++--
assets/email_template.html | 142 ++++++++++++------
assets/multiqc_config.yaml | 11 --
assets/multiqc_config.yml | 11 ++
assets/schema_input.json | 5 +-
docs/README.md | 8 +-
docs/output.md | 28 ++--
docs/usage.md | 109 +++++++-------
modules.json | 8 +-
.../custom/dumpsoftwareversions/main.nf | 3 +
.../custom/dumpsoftwareversions/meta.yml | 2 +-
modules/nf-core/modules/fastqc/main.nf | 3 +
modules/nf-core/modules/fastqc/meta.yml | 90 +++++------
modules/nf-core/modules/multiqc/main.nf | 9 +-
modules/nf-core/modules/multiqc/meta.yml | 66 ++++----
nextflow_schema.json | 14 +-
workflows/hic.nf | 2 +-
33 files changed, 361 insertions(+), 382 deletions(-)
delete mode 100644 .markdownlint.yml
create mode 100644 .prettierrc.yml
delete mode 100644 .yamllint.yml
delete mode 100644 assets/multiqc_config.yaml
create mode 100644 assets/multiqc_config.yml
diff --git a/.editorconfig b/.editorconfig
index 9554950..b6b3190 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,12 +8,9 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
-[*.{yml,yaml}]
+[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2
-[*.json]
-insert_final_newline = unset
-
# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 383bc0e..21343c4 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)
If you'd like to write some code for nf-core/hic, the standard workflow is as follows:
-1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid duplicating work
- * If there isn't one already, please create one so that others know you're working on this
+1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/hic repository](https://github.com/nf-core/hic) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
@@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als
:warning: Only in the unlikely and regretful event of a release happening with a bug.
-* On your own fork, make a new branch `patch` based on `upstream/master`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
## Getting help
@@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards:
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
### Default values
@@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces
Please use the following naming schemes, to make it easy to understand what is going where.
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
### Nextflow version bumping
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 8e439f4..98a7950 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,7 +2,6 @@ name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
-
- type: markdown
attributes:
value: |
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 8b36133..f4aec89 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,10 +16,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+ - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+ - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index cacd11e..303d385 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -18,7 +18,6 @@ jobs:
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
-
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index d15b4b8..d319986 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -10,9 +10,9 @@ jobs:
if: github.repository == 'nf-core/hic'
runs-on: ubuntu-latest
steps:
+ # Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
-
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 3521022..3636672 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,8 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/hic'
run: |
- { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
+ "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
@@ -43,4 +42,4 @@ jobs:
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
-
+#
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 64b9e73..4940ecf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,18 +16,18 @@ jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
- if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hic') }}
+ if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hic') }}"
runs-on: ubuntu-latest
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- - NXF_VER: '21.10.3'
- NXF_EDGE: ''
+ - NXF_VER: "21.10.3"
+ NXF_EDGE: ""
# Test latest edge release of Nextflow
- - NXF_VER: ''
- NXF_EDGE: '1'
+ - NXF_VER: ""
+ NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
@@ -48,3 +48,5 @@ jobs:
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+#
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index fda934c..e9cf5de 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,7 @@
name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
on:
push:
pull_request:
@@ -8,42 +9,6 @@ on:
types: [published]
jobs:
- Markdown:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-node@v2
- - name: Install markdownlint
- run: npm install -g markdownlint-cli
- - name: Run Markdownlint
- run: markdownlint .
-
- # If the above check failed, post a comment on the PR explaining the failure
- - name: Post PR comment
- if: failure()
- uses: mshick/add-pr-comment@v1
- with:
- message: |
- ## Markdown linting is failing
-
- To keep the code consistent with lots of contributors, we run automated code consistency checks.
- To fix this CI test, please run:
-
- * Install `markdownlint-cli`
- * On Mac: `brew install markdownlint-cli`
- * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
- * Fix the markdown errors
- * Automatically: `markdownlint . --fix`
- * Manually resolve anything left from `markdownlint .`
-
- Once you push these changes the test should pass, and you can hide this comment :+1:
-
- We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
- Thanks again for your contribution!
- repo-token: ${{ secrets.GITHUB_TOKEN }}
- allow-repeats: false
-
EditorConfig:
runs-on: ubuntu-latest
steps:
@@ -55,49 +20,24 @@ jobs:
run: npm install -g editorconfig-checker
- name: Run ECLint check
- run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+ run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
- YAML:
+ Prettier:
runs-on: ubuntu-latest
steps:
- - name: Checkout
- uses: actions/checkout@master
- - name: 'Yamllint'
- uses: karancode/yamllint-github-action@master
- with:
- yamllint_file_or_dir: '.'
- yamllint_config_filepath: '.yamllint.yml'
-
- # If the above check failed, post a comment on the PR explaining the failure
- - name: Post PR comment
- if: failure()
- uses: mshick/add-pr-comment@v1
- with:
- message: |
- ## YAML linting is failing
-
- To keep the code consistent with lots of contributors, we run automated code consistency checks.
- To fix this CI test, please run:
-
- * Install `yamllint`
- * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
- instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
- * Fix the markdown errors
- * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
- * Fix any reported errors in your YAML files
+ - uses: actions/checkout@v2
- Once you push these changes the test should pass, and you can hide this comment :+1:
+ - uses: actions/setup-node@v2
- We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+ - name: Install Prettier
+ run: npm install -g prettier
- Thanks again for your contribution!
- repo-token: ${{ secrets.GITHUB_TOKEN }}
- allow-repeats: false
+ - name: Run Prettier --check
+ run: prettier --check ${GITHUB_WORKSPACE}
nf-core:
runs-on: ubuntu-latest
steps:
-
- name: Check out pipeline code
uses: actions/checkout@v2
@@ -110,8 +50,8 @@ jobs:
- uses: actions/setup-python@v1
with:
- python-version: '3.6'
- architecture: 'x64'
+ python-version: "3.6"
+ architecture: "x64"
- name: Install dependencies
run: |
@@ -139,3 +79,4 @@ jobs:
lint_results.md
PR_number.txt
+#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 44d7299..91c487a 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -1,4 +1,3 @@
-
name: nf-core linting comment
# This workflow is triggered after the linting action is complete
# It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +26,4 @@ jobs:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
path: linting-logs/lint_results.md
-
+#
diff --git a/.gitpod.yml b/.gitpod.yml
index b7d4cee..c452ee9 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -2,13 +2,13 @@ image: nfcore/gitpod:latest
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- - codezombiech.gitignore # Language support for .gitignore files
+ - codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer #Â SVG viewer
- - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
- - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+ - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
+ - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+ - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+ - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+ - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
- - oderwat.indent-rainbow # Highlight indentation level
- - streetsidesoftware.code-spell-checker # Spelling checker for source code
+ - oderwat.indent-rainbow # Highlight indentation level
+ - streetsidesoftware.code-spell-checker # Spelling checker for source code
diff --git a/.markdownlint.yml b/.markdownlint.yml
deleted file mode 100644
index 9e605fc..0000000
--- a/.markdownlint.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-# Markdownlint configuration file
-default: true
-line-length: false
-ul-indent:
- indent: 4
-no-duplicate-header:
- siblings_only: true
-no-inline-html:
- allowed_elements:
- - img
- - p
- - kbd
- - details
- - summary
diff --git a/.prettierrc.yml b/.prettierrc.yml
new file mode 100644
index 0000000..c81f9a7
--- /dev/null
+++ b/.prettierrc.yml
@@ -0,0 +1 @@
+printWidth: 120
diff --git a/.yamllint.yml b/.yamllint.yml
deleted file mode 100644
index d466dee..0000000
--- a/.yamllint.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-extends: default
-
-rules:
- document-start: disable
- line-length: disable
- truthy: disable
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 87c2402..9dd2005 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) te
### `Fixed`
+- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler
+
### `Dependencies`
### `Deprecated`
diff --git a/CITATIONS.md b/CITATIONS.md
index 557e1f8..07d08ce 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,23 +10,26 @@
## Pipeline tools
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-* [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.
+- [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.
## Software packaging/containerisation tools
-* [Anaconda](https://anaconda.com)
- > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+- [Anaconda](https://anaconda.com)
-* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
- > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+ > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
-* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
- > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
-* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+ > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
-* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
- > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+
+ > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+ > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
diff --git a/README.md b/README.md
index b7a2836..eefaec9 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-#  
+#  
[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+CI%22)
[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+linting%22)
@@ -17,11 +17,13 @@
## Introduction
<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
+
**nf-core/hic** is a bioinformatics best-practice analysis pipeline for Analysis of Chromosome Conformation Capture data (Hi-C).
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
+
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
## Pipeline summary
@@ -35,28 +37,28 @@ On release, automated continuous integration tests run the pipeline on a full-si
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
3. Download the pipeline and test it on a minimal dataset with a single command:
- ```console
- nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
- ```
+ ```console
+ nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
+ ```
- Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+ Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
- > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
- > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
- > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
- > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+ > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
+ > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+ > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+ > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
4. Start running your own analysis!
- <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+ <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
- ```console
- nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
- ```
+ ```console
+ nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+ ```
## Documentation
@@ -82,6 +84,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
<!-- If you use nf-core/hic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
You can cite the `nf-core` publication as follows:
diff --git a/assets/email_template.html b/assets/email_template.html
index d207f01..80d5dac 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -1,53 +1,111 @@
<html>
-<head>
- <meta charset="utf-8">
- <meta http-equiv="X-UA-Compatible" content="IE=edge">
- <meta name="viewport" content="width=device-width, initial-scale=1">
+ <head>
+ <meta charset="utf-8" />
+ <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+ <meta name="viewport" content="width=device-width, initial-scale=1" />
- <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)">
- <title>nf-core/hic Pipeline Report</title>
-</head>
-<body>
-<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+ <!-- prettier-ignore -->
+ <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)" />
+ <title>nf-core/hic Pipeline Report</title>
+ </head>
+ <body>
+ <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
+ <img src="cid:nfcorepipelinelogo" />
-<img src="cid:nfcorepipelinelogo">
+ <h1>nf-core/hic v${version}</h1>
+ <h2>Run Name: $runName</h2>
-<h1>nf-core/hic v${version}</h1>
-<h2>Run Name: $runName</h2>
-
-<% if (!success){
- out << """
- <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
- <h4 style="margin-top:0; color: inherit;">nf-core/hic execution completed unsuccessfully!</h4>
+ <% if (!success){ out << """
+ <div
+ style="
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #ebccd1;
+ padding: 15px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+ border-radius: 4px;
+ "
+ >
+ <h4 style="margin-top: 0; color: inherit">nf-core/hic execution completed unsuccessfully!</h4>
<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
<p>The full error message was:</p>
- <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
- </div>
- """
-} else {
- out << """
- <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+ <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
+ </div>
+ """ } else { out << """
+ <div
+ style="
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+ padding: 15px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+ border-radius: 4px;
+ "
+ >
nf-core/hic execution completed successfully!
- </div>
- """
-}
-%>
+ </div>
+ """ } %>
-<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-<p>The command used to launch the workflow was as follows:</p>
-<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
+ <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+ <p>The command used to launch the workflow was as follows:</p>
+ <pre
+ style="
+ white-space: pre-wrap;
+ overflow: visible;
+ background-color: #ededed;
+ padding: 15px;
+ border-radius: 4px;
+ margin-bottom: 30px;
+ "
+ >
+$commandLine</pre
+ >
-<h3>Pipeline Configuration:</h3>
-<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
- <tbody style="border-bottom: 1px solid #ddd;">
- <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
- </tbody>
-</table>
+ <h3>Pipeline Configuration:</h3>
+ <table
+ style="
+ width: 100%;
+ max-width: 100%;
+ border-spacing: 0;
+ border-collapse: collapse;
+ border: 0;
+ margin-bottom: 30px;
+ "
+ >
+ <tbody style="border-bottom: 1px solid #ddd">
+ <% out << summary.collect{ k,v -> "
+ <tr>
+ <th
+ style="
+ text-align: left;
+ padding: 8px 0;
+ line-height: 1.42857143;
+ vertical-align: top;
+ border-top: 1px solid #ddd;
+ "
+ >
+ $k
+ </th>
+ <td
+ style="
+ text-align: left;
+ padding: 8px;
+ line-height: 1.42857143;
+ vertical-align: top;
+ border-top: 1px solid #ddd;
+ "
+ >
+ <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
+ </td>
+ </tr>
+ " }.join("\n") %>
+ </tbody>
+ </table>
-<p>nf-core/hic</p>
-<p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
-
-</div>
-
-</body>
+ <p>nf-core/hic</p>
+ <p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
+ </div>
+ </body>
</html>
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
deleted file mode 100644
index c05ad14..0000000
--- a/assets/multiqc_config.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-report_comment: >
- This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
- analysis pipeline. For information about how to interpret these results, please see the
- <a href="https://nf-co.re/hic" target="_blank">documentation</a>.
-report_section_order:
- software_versions:
- order: -1000
- nf-core-hic-summary:
- order: -1001
-
-export_plots: true
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
new file mode 100644
index 0000000..e371ccf
--- /dev/null
+++ b/assets/multiqc_config.yml
@@ -0,0 +1,11 @@
+report_comment: >
+ This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
+ analysis pipeline. For information about how to interpret these results, please see the
+ <a href="https://nf-co.re/hic" target="_blank">documentation</a>.
+report_section_order:
+ software_versions:
+ order: -1000
+ "nf-core-hic-summary":
+ order: -1001
+
+export_plots: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1c3f0f7..fae1a32 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -31,9 +31,6 @@
]
}
},
- "required": [
- "sample",
- "fastq_1"
- ]
+ "required": ["sample", "fastq_1"]
}
}
diff --git a/docs/README.md b/docs/README.md
index 112811a..d673c50 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -2,9 +2,9 @@
The nf-core/hic documentation is split into the following pages:
-* [Usage](usage.md)
- * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
-* [Output](output.md)
- * An overview of the different results produced by the pipeline and how to interpret them.
+- [Usage](usage.md)
+ - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
+- [Output](output.md)
+ - An overview of the different results produced by the pipeline and how to interpret them.
You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
diff --git a/docs/output.md b/docs/output.md
index 57dce62..0a1b036 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -12,18 +12,18 @@ 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
-* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
-* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [FastQC](#fastqc) - Raw read QC
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
### FastQC
<details markdown="1">
<summary>Output files</summary>
-* `fastqc/`
- * `*_fastqc.html`: FastQC report containing quality metrics.
- * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+- `fastqc/`
+ - `*_fastqc.html`: FastQC report containing quality metrics.
+ - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
</details>
@@ -42,10 +42,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
<details markdown="1">
<summary>Output files</summary>
-* `multiqc/`
- * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
- * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
- * `multiqc_plots/`: directory containing static images from the report in various formats.
+- `multiqc/`
+ - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+ - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+ - `multiqc_plots/`: directory containing static images from the report in various formats.
</details>
@@ -58,10 +58,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
<details markdown="1">
<summary>Output files</summary>
-* `pipeline_info/`
- * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
- * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
- * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+- `pipeline_info/`
+ - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+ - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+ - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
</details>
diff --git a/docs/usage.md b/docs/usage.md
index e7e1c41..e106ac9 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -44,11 +44,11 @@ TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
```
-| Column | Description |
-|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
-| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
+| Column | Description |
+| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
+| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
@@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:
```console
-nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
+nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
```
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -65,9 +65,9 @@ This will launch the pipeline with the `docker` configuration profile. See below
Note that the pipeline will create the following files in your working directory:
```console
-work # Directory containing the nextflow working files
-results # Finished results (configurable, see below)
-.nextflow_log # Log file from Nextflow
+work # Directory containing the nextflow working files
+<OUTIDR> # Finished results in specified location (defined with --outdir)
+.nextflow_log # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```
@@ -106,25 +106,25 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles.
If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended.
-* `docker`
- * A generic configuration profile to be used with [Docker](https://docker.com/)
-* `singularity`
- * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
-* `podman`
- * A generic configuration profile to be used with [Podman](https://podman.io/)
-* `shifter`
- * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
-* `charliecloud`
- * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
-* `conda`
- * A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-* `test`
- * A profile with a complete configuration for automated testing
- * Includes links to test data so needs no other parameters
+- `docker`
+ - A generic configuration profile to be used with [Docker](https://docker.com/)
+- `singularity`
+ - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
+- `podman`
+ - A generic configuration profile to be used with [Podman](https://podman.io/)
+- `shifter`
+ - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
+- `charliecloud`
+ - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+- `conda`
+ - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
+- `test`
+ - A profile with a complete configuration for automated testing
+ - Includes links to test data so needs no other parameters
### `-resume`
-Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
+Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html).
You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
@@ -186,6 +186,7 @@ process {
```
> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
+>
> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
### Updating containers
@@ -196,35 +197,35 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
3. Create the custom config accordingly:
- * For Docker:
-
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
-
- * For Singularity:
-
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
-
- * For Conda:
-
- ```nextflow
- process {
- withName: PANGOLIN {
- conda = 'bioconda::pangolin=3.0.5'
- }
- }
- ```
+ - For Docker:
+
+ ```nextflow
+ process {
+ withName: PANGOLIN {
+ container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
+ }
+ }
+ ```
+
+ - For Singularity:
+
+ ```nextflow
+ process {
+ withName: PANGOLIN {
+ container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
+ }
+ }
+ ```
+
+ - For Conda:
+
+ ```nextflow
+ process {
+ withName: PANGOLIN {
+ conda = 'bioconda::pangolin=3.0.5'
+ }
+ }
+ ```
> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
diff --git a/modules.json b/modules.json
index 2233ec4..bd45115 100644
--- a/modules.json
+++ b/modules.json
@@ -4,14 +4,14 @@
"repos": {
"nf-core/modules": {
"custom/dumpsoftwareversions": {
- "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"fastqc": {
- "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"multiqc": {
- "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}
}
}
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
index 934bb46..327d510 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
path "software_versions_mqc.yml", emit: mqc_yml
path "versions.yml" , emit: versions
+ when:
+ task.ext.when == null || task.ext.when
+
script:
def args = task.ext.args ?: ''
template 'dumpsoftwareversions.py'
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
index 5b5b8a6..60b546a 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
@@ -8,7 +8,7 @@ tools:
description: Custom module used to dump software versions within the nf-core pipeline template
homepage: https://github.com/nf-core/tools
documentation: https://github.com/nf-core/tools
- licence: ['MIT']
+ licence: ["MIT"]
input:
- versions:
type: file
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
index d250eca..ed6b8c5 100644
--- a/modules/nf-core/modules/fastqc/main.nf
+++ b/modules/nf-core/modules/fastqc/main.nf
@@ -15,6 +15,9 @@ process FASTQC {
tuple val(meta), path("*.zip") , emit: zip
path "versions.yml" , emit: versions
+ when:
+ task.ext.when == null || task.ext.when
+
script:
def args = task.ext.args ?: ''
// Add soft-links to original FastQs for consistent naming in pipeline
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml
index b09553a..4da5bb5 100644
--- a/modules/nf-core/modules/fastqc/meta.yml
+++ b/modules/nf-core/modules/fastqc/meta.yml
@@ -1,52 +1,52 @@
name: fastqc
description: Run FastQC on sequenced reads
keywords:
- - quality control
- - qc
- - adapters
- - fastq
+ - quality control
+ - qc
+ - adapters
+ - fastq
tools:
- - fastqc:
- description: |
- FastQC gives general quality metrics about your reads.
- It provides information about the quality score distribution
- across your reads, the per base sequence content (%A/C/G/T).
- You get information about adapter contamination and other
- overrepresented sequences.
- homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
- licence: ['GPL-2.0-only']
+ - fastqc:
+ description: |
+ FastQC gives general quality metrics about your reads.
+ It provides information about the quality score distribution
+ across your reads, the per base sequence content (%A/C/G/T).
+ You get information about adapter contamination and other
+ overrepresented sequences.
+ homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+ licence: ["GPL-2.0-only"]
input:
- - meta:
- type: map
- description: |
- Groovy Map containing sample information
- e.g. [ id:'test', single_end:false ]
- - reads:
- type: file
- description: |
- List of input FastQ files of size 1 and 2 for single-end and paired-end data,
- respectively.
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - reads:
+ type: file
+ description: |
+ List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+ respectively.
output:
- - meta:
- type: map
- description: |
- Groovy Map containing sample information
- e.g. [ id:'test', single_end:false ]
- - html:
- type: file
- description: FastQC report
- pattern: "*_{fastqc.html}"
- - zip:
- type: file
- description: FastQC report archive
- pattern: "*_{fastqc.zip}"
- - versions:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - html:
+ type: file
+ description: FastQC report
+ pattern: "*_{fastqc.html}"
+ - zip:
+ type: file
+ description: FastQC report archive
+ pattern: "*_{fastqc.zip}"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
authors:
- - "@drpatelh"
- - "@grst"
- - "@ewels"
- - "@FelixKrueger"
+ - "@drpatelh"
+ - "@grst"
+ - "@ewels"
+ - "@FelixKrueger"
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf
index 3dceb16..1264aac 100644
--- a/modules/nf-core/modules/multiqc/main.nf
+++ b/modules/nf-core/modules/multiqc/main.nf
@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_medium'
- conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
+ conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
input:
path multiqc_files
@@ -15,6 +15,9 @@ process MULTIQC {
path "*_plots" , optional:true, emit: plots
path "versions.yml" , emit: versions
+ when:
+ task.ext.when == null || task.ext.when
+
script:
def args = task.ext.args ?: ''
"""
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml
index 63c75a4..6fa891e 100644
--- a/modules/nf-core/modules/multiqc/meta.yml
+++ b/modules/nf-core/modules/multiqc/meta.yml
@@ -1,40 +1,40 @@
name: MultiQC
description: Aggregate results from bioinformatics analyses across many samples into a single report
keywords:
- - QC
- - bioinformatics tools
- - Beautiful stand-alone HTML report
+ - QC
+ - bioinformatics tools
+ - Beautiful stand-alone HTML report
tools:
- - multiqc:
- description: |
- MultiQC searches a given directory for analysis logs and compiles a HTML report.
- It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
- homepage: https://multiqc.info/
- documentation: https://multiqc.info/docs/
- licence: ['GPL-3.0-or-later']
+ - multiqc:
+ description: |
+ MultiQC searches a given directory for analysis logs and compiles a HTML report.
+ It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+ homepage: https://multiqc.info/
+ documentation: https://multiqc.info/docs/
+ licence: ["GPL-3.0-or-later"]
input:
- - multiqc_files:
- type: file
- description: |
- List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+ - multiqc_files:
+ type: file
+ description: |
+ List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
output:
- - report:
- type: file
- description: MultiQC report file
- pattern: "multiqc_report.html"
- - data:
- type: dir
- description: MultiQC data dir
- pattern: "multiqc_data"
- - plots:
- type: file
- description: Plots created by MultiQC
- pattern: "*_data"
- - versions:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
+ - report:
+ type: file
+ description: MultiQC report file
+ pattern: "multiqc_report.html"
+ - data:
+ type: dir
+ description: MultiQC data dir
+ pattern: "multiqc_data"
+ - plots:
+ type: file
+ description: Plots created by MultiQC
+ pattern: "*_data"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
authors:
- - "@abhi18av"
- - "@bunop"
- - "@drpatelh"
+ - "@abhi18av"
+ - "@bunop"
+ - "@drpatelh"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b2c0603..9d007fa 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,10 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
- "required": [
- "input",
- "outdir"
- ],
+ "required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
@@ -185,14 +182,7 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
- "enum": [
- "symlink",
- "rellink",
- "link",
- "copy",
- "copyNoFollow",
- "move"
- ],
+ "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 5cb900f..7c469dd 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -23,7 +23,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
/*
--
GitLab