From 46edf5c29cffb02d67818fa349ed0e845acdc2f8 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 12 Dec 2024 11:25:00 +0000
Subject: [PATCH 1/3] Template update for nf-core/tools version 3.1.0
---
.github/CONTRIBUTING.md | 12 +-
.github/workflows/awsfulltest.yml | 21 +-
.github/workflows/branch.yml | 18 +-
.github/workflows/ci.yml | 2 +-
.github/workflows/download_pipeline.yml | 8 +-
.github/workflows/fix-linting.yml | 4 +-
.github/workflows/linting.yml | 10 +-
.github/workflows/linting_comment.yml | 2 +-
.github/workflows/release-announcements.yml | 2 +-
.../workflows/template_version_comment.yml | 2 +-
.gitpod.yml | 11 +-
.nf-core.yml | 8 +-
.vscode/settings.json | 3 +
conf/base.config | 2 +-
conf/igenomes.config | 440 ------------------
conf/igenomes_ignored.config | 9 -
conf/modules.config | 1 +
conf/test.config | 3 +-
conf/test_full.config | 4 +-
docs/usage.md | 35 +-
main.nf | 13 -
modules.json | 8 +-
modules/nf-core/fastqc/main.nf | 2 +-
modules/nf-core/fastqc/meta.yml | 1 +
nextflow.config | 61 ++-
nextflow_schema.json | 49 +-
ro-crate-metadata.json | 313 +++++++++++++
.../utils_nfcore_viralrecon_pipeline/main.nf | 43 +-
.../nf-core/utils_nextflow_pipeline/main.nf | 2 +
.../tests/main.workflow.nf.test | 10 +-
.../nf-core/utils_nfcore_pipeline/main.nf | 89 +---
.../tests/main.function.nf.test | 46 +-
.../tests/main.function.nf.test.snap | 30 --
.../utils_nfschema_plugin/tests/main.nf.test | 4 +-
workflows/viralrecon.nf | 2 +-
35 files changed, 499 insertions(+), 771 deletions(-)
create mode 100644 .vscode/settings.json
delete mode 100644 conf/igenomes.config
delete mode 100644 conf/igenomes_ignored.config
create mode 100644 ro-crate-metadata.json
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 3625c003..9a05a483 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/viralrecon: Contributing Guidelines
+# `nf-core/viralrecon`: Contributing Guidelines
Hi there!
Many thanks for taking an interest in improving nf-core/viralrecon.
@@ -55,9 +55,9 @@ 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`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `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.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
## Getting help
@@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/viralrecon documentati
## Pipeline contribution conventions
-To make the nf-core/viralrecon code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/viralrecon` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
### Adding a new step
If you wish to contribute a new step, please use the following coding standards:
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
### Default values
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 0d4faddf..8509928e 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,11 +1,12 @@
name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on AWS batch
on:
pull_request:
branches:
+ - main
- master
workflow_dispatch:
pull_request_review:
@@ -18,18 +19,30 @@ jobs:
if: github.repository == 'nf-core/viralrecon' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
steps:
- - uses: octokit/request-action@v2.x
+ - name: Get PR reviews
+ uses: octokit/request-action@v2.x
+ if: github.event_name != 'workflow_dispatch'
id: check_approvals
+ continue-on-error: true
with:
- route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+ route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- - id: test_variables
+
+ - name: Check for approvals
+ if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+ run: |
+ echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+ exit 1
+
+ - name: Check for enough approvals (>=2)
+ id: test_variables
if: github.event_name != 'workflow_dispatch'
run: |
JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index ce44d6b2..e9485576 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
on:
pull_request_target:
- branches: [master]
+ branches:
+ - main
+ - master
jobs:
test:
runs-on: ubuntu-latest
steps:
- # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+ # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
- name: Check PRs
if: github.repository == 'nf-core/viralrecon'
run: |
@@ -22,7 +24,7 @@ jobs:
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
- ## This PR is against the `master` branch :x:
+ ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
* Do not close this PR
* Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
Hi @${{ github.event.pull_request.user.login }},
- It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
- The `master` branch on nf-core repositories should always contain code from the latest release.
- Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+ It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+ The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+ Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f8294d2b..41804f58 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
profile: "singularity"
steps:
- name: Check out pipeline code
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 713dc3e7..2576cc0c 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
# Run the workflow when:
# - dispatched manually
-# - when a PR is opened or reopened to master branch
+# - when a PR is opened or reopened to main/master branch
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
@@ -17,9 +17,11 @@ on:
- edited
- synchronize
branches:
+ - main
- master
pull_request_target:
branches:
+ - main
- master
env:
@@ -35,7 +37,7 @@ jobs:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+ - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.12"
architecture: "x64"
@@ -69,7 +71,7 @@ jobs:
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
--container-system 'singularity' \
- --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+ --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
--container-cache-utilisation 'amend' \
--download-configuration 'yes'
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 85c55435..572aa337 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+ - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}
@@ -32,7 +32,7 @@ jobs:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
# Install and run pre-commit
- - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+ - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.12"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a502573c..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+ - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Set up Python 3.12
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+ uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.12"
@@ -31,12 +31,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
- - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+ - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.12"
architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
- name: Upload linting log file artifact
if: ${{ always() }}
- uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+ uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: linting-logs
path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 42e519bf..0bed96d3 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
- uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+ uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
with:
workflow: linting.yml
workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index c6ba35df..450b1d5e 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+ - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.10"
- name: Install dependencies
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index e8aafe44..537529bc 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -9,7 +9,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
ref: ${{ github.event.pull_request.head.sha }}
diff --git a/.gitpod.yml b/.gitpod.yml
index 46118637..83599f63 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,12 +6,5 @@ tasks:
nextflow self-update
vscode:
- extensions: # based on nf-core.nf-core-extensionpack
- #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- - 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
- - charliermarsh.ruff # Code linter Ruff
+ extensions:
+ - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index a928217a..cd2763f2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,10 +1,8 @@
-bump_version: null
lint:
files_unchanged:
- assets/email_template.html
- assets/email_template.txt
-nf_core_version: 3.0.2
-org_path: null
+nf_core_version: 3.1.0
repository_type: pipeline
template:
author: Patel H, Varona S and Monzon S
@@ -14,6 +12,6 @@ template:
name: viralrecon
org: nf-core
outdir: .
- skip_features: null
+ skip_features:
+ - igenomes
version: 2.7.0dev
-update: null
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 00000000..a33b527c
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+ "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/conf/base.config b/conf/base.config
index 46b66dcd..6878cd46 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -20,7 +20,7 @@ process {
maxErrors = '-1'
// Process-specific resource requirements
- // NOTE - Please try and re-use the labels below as much as possible.
+ // NOTE - Please try and reuse the labels below as much as possible.
// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
// If possible, it would be nice to keep the same label naming convention when
// adding in your local modules too.
diff --git a/conf/igenomes.config b/conf/igenomes.config
deleted file mode 100644
index 3f114377..00000000
--- a/conf/igenomes.config
+++ /dev/null
@@ -1,440 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Nextflow config file for iGenomes paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Defines reference genomes using iGenome paths.
- Can be used by any config that customises the base path using:
- $params.igenomes_base / --igenomes_base
-----------------------------------------------------------------------------------------
-*/
-
-params {
- // illumina iGenomes reference file paths
- genomes {
- 'GRCh37' {
- fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
- mito_name = "MT"
- macs_gsize = "2.7e9"
- blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
- }
- 'GRCh38' {
- fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- macs_gsize = "2.7e9"
- blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
- }
- 'CHM13' {
- fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
- bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
- gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
- gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
- mito_name = "chrM"
- }
- 'GRCm38' {
- fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
- mito_name = "MT"
- macs_gsize = "1.87e9"
- blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
- }
- 'TAIR10' {
- fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
- mito_name = "Mt"
- }
- 'EB2' {
- fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
- }
- 'UMD3.1' {
- fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
- mito_name = "MT"
- }
- 'WBcel235' {
- fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
- mito_name = "MtDNA"
- macs_gsize = "9e7"
- }
- 'CanFam3.1' {
- fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
- mito_name = "MT"
- }
- 'GRCz10' {
- fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
- mito_name = "MT"
- }
- 'BDGP6' {
- fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
- mito_name = "M"
- macs_gsize = "1.2e8"
- }
- 'EquCab2' {
- fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
- mito_name = "MT"
- }
- 'EB1' {
- fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
- }
- 'Galgal4' {
- fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
- mito_name = "MT"
- }
- 'Gm01' {
- fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
- }
- 'Mmul_1' {
- fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
- mito_name = "MT"
- }
- 'IRGSP-1.0' {
- fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
- mito_name = "Mt"
- }
- 'CHIMP2.1.4' {
- fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
- mito_name = "MT"
- }
- 'Rnor_5.0' {
- fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
- mito_name = "MT"
- }
- 'Rnor_6.0' {
- fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
- mito_name = "MT"
- }
- 'R64-1-1' {
- fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
- mito_name = "MT"
- macs_gsize = "1.2e7"
- }
- 'EF2' {
- fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
- mito_name = "MT"
- macs_gsize = "1.21e7"
- }
- 'Sbi1' {
- fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
- }
- 'Sscrofa10.2' {
- fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
- mito_name = "MT"
- }
- 'AGPv3' {
- fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
- mito_name = "Mt"
- }
- 'hg38' {
- fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- macs_gsize = "2.7e9"
- blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
- }
- 'hg19' {
- fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
- mito_name = "chrM"
- macs_gsize = "2.7e9"
- blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
- }
- 'mm10' {
- fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
- mito_name = "chrM"
- macs_gsize = "1.87e9"
- blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
- }
- 'bosTau8' {
- fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- }
- 'ce10' {
- fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
- mito_name = "chrM"
- macs_gsize = "9e7"
- }
- 'canFam3' {
- fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
- mito_name = "chrM"
- }
- 'danRer10' {
- fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- macs_gsize = "1.37e9"
- }
- 'dm6' {
- fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- macs_gsize = "1.2e8"
- }
- 'equCab2' {
- fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
- mito_name = "chrM"
- }
- 'galGal4' {
- fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
- mito_name = "chrM"
- }
- 'panTro4' {
- fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
- mito_name = "chrM"
- }
- 'rn6' {
- fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
- mito_name = "chrM"
- }
- 'sacCer3' {
- fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
- readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
- mito_name = "chrM"
- macs_gsize = "1.2e7"
- }
- 'susScr3' {
- fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
- bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
- bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
- star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
- bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
- gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
- bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
- readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
- mito_name = "chrM"
- }
- }
-}
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
deleted file mode 100644
index b4034d82..00000000
--- a/conf/igenomes_ignored.config
+++ /dev/null
@@ -1,9 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Nextflow config file for iGenomes paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Empty genomes dictionary to use when igenomes is ignored.
-----------------------------------------------------------------------------------------
-*/
-
-params.genomes = [:]
diff --git a/conf/modules.config b/conf/modules.config
index d266a387..d203d2b6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,6 +21,7 @@ process {
withName: FASTQC {
ext.args = '--quiet'
}
+
withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
diff --git a/conf/test.config b/conf/test.config
index 430b4e5f..0b4d5555 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -27,6 +27,5 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
- // Genome references
- genome = 'R64-1-1'
+
}
diff --git a/conf/test_full.config b/conf/test_full.config
index 3aa3ddb6..446d46a1 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -19,6 +19,6 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
- // Genome references
- genome = 'R64-1-1'
+ // Fasta references
+ fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
}
diff --git a/docs/usage.md b/docs/usage.md
index 7263e3f3..f5fb5239 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -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:
```bash
-nextflow run nf-core/viralrecon --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run nf-core/viralrecon --input ./samplesheet.csv --outdir ./results -profile docker
```
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
The above pipeline run specified with a params file in yaml format:
@@ -90,7 +89,6 @@ with:
```yaml title="params.yaml"
input: './samplesheet.csv'
outdir: './results/'
-genome: 'GRCh37'
<...>
```
@@ -106,23 +104,21 @@ nextflow pull nf-core/viralrecon
### Reproducibility
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
First, go to the [nf-core/viralrecon releases page](https://github.com/nf-core/viralrecon/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
## Core Nextflow arguments
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
### `-profile`
@@ -130,16 +126,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur
Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
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, since it can lead to different results on different machines dependent on the computer enviroment.
+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, since it can lead to different results on different machines dependent on the computer environment.
- `test`
- A profile with a complete configuration for automated testing
@@ -175,13 +170,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
### Resource requests
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
### Custom Containers
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
diff --git a/main.nf b/main.nf
index 5cf74e5c..49daf379 100644
--- a/main.nf
+++ b/main.nf
@@ -18,19 +18,6 @@
include { VIRALRECON } from './workflows/viralrecon'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_viralrecon_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_viralrecon_pipeline'
-include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_viralrecon_pipeline'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- GENOME PARAMETER VALUES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-// TODO nf-core: Remove this line if you don't need a FASTA file
-// This is an example of how to use getGenomeAttribute() to fetch parameters
-// from igenomes.config using `--genome`
-params.fasta = getGenomeAttribute('fasta')
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
diff --git a/modules.json b/modules.json
index 9982e22e..c86576f9 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
"nf-core": {
"fastqc": {
"branch": "master",
- "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+ "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
"installed_by": ["modules"]
},
"multiqc": {
@@ -21,17 +21,17 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
- "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+ "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
- "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+ "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
- "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+ "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
"installed_by": ["subworkflows"]
}
}
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d8989f48..752c3a10 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -24,7 +24,7 @@ process FASTQC {
// Make list of old name and new name pairs to use for renaming in the bash while loop
def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
def rename_to = old_new_pairs*.join(' ').join(' ')
- def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+ def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
// The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
// https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4827da7a..2b2e62b8 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,6 +11,7 @@ tools:
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/
diff --git a/nextflow.config b/nextflow.config
index e59f91c2..897dcdf2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,11 +13,6 @@ params {
// Input options
input = null
- // References
- genome = null
- igenomes_base = 's3://ngi-igenomes/igenomes/'
- igenomes_ignore = false
-
// MultiQC options
multiqc_config = null
multiqc_title = null
@@ -38,8 +33,7 @@ params {
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
- // Config options
+ trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
config_profile_name = null
config_profile_description = null
@@ -153,6 +147,13 @@ profiles {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
+ process {
+ resourceLimits = [
+ memory: 8.GB,
+ cpus : 4,
+ time : 1.h
+ ]
+ }
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
@@ -174,8 +175,7 @@ podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
-// Load igenomes.config if required
-includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
+
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -201,30 +201,49 @@ set -C # No clobber - prevent output redirection from overwriting files.
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
- file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
- file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
- file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+ file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
- file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'nf-core/viralrecon'
- author = """Patel H, Varona S and Monzon S"""
+ author = """Patel H, Varona S and Monzon S""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+ contributors = [
+ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+ [
+ name: 'Patel H',
+ affiliation: '',
+ email: '',
+ github: '',
+ contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+ orcid: ''
+ ],
+ [
+ name: ' Varona S and Monzon S',
+ affiliation: '',
+ email: '',
+ github: '',
+ contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+ orcid: ''
+ ],
+ ]
homePage = 'https://github.com/nf-core/viralrecon'
description = """Assembly and intrahost/low-frequency variant calling for viral samples"""
mainScript = 'main.nf'
+ defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '2.7.0dev'
doi = ''
@@ -237,9 +256,10 @@ plugins {
validation {
defaultIgnoreParams = ["genomes"]
+ monochromeLogs = params.monochrome_logs
help {
enabled = true
- command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+ command = "nextflow run nf-core/viralrecon -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
@@ -249,15 +269,15 @@ validation {
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
-\033[0;35m ${manifest.name} ${manifest.version}\033[0m
+\033[0;35m nf-core/viralrecon ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
- afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+ afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
- https://github.com/${manifest.name}/blob/master/CITATIONS.md
+ https://github.com/nf-core/viralrecon/blob/master/CITATIONS.md
"""
}
summary {
@@ -265,6 +285,3 @@ validation {
afterText = validation.help.afterText
}
}
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e3e6cc94..5fbb6cc5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -43,45 +43,6 @@
}
}
},
- "reference_genome_options": {
- "title": "Reference genome options",
- "type": "object",
- "fa_icon": "fas fa-dna",
- "description": "Reference genome related files and options required for the workflow.",
- "properties": {
- "genome": {
- "type": "string",
- "description": "Name of iGenomes reference.",
- "fa_icon": "fas fa-book",
- "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
- },
- "fasta": {
- "type": "string",
- "format": "file-path",
- "exists": true,
- "mimetype": "text/plain",
- "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
- "description": "Path to FASTA genome file.",
- "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
- "fa_icon": "far fa-file-code"
- },
- "igenomes_ignore": {
- "type": "boolean",
- "description": "Do not load the iGenomes reference config.",
- "fa_icon": "fas fa-ban",
- "hidden": true,
- "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
- },
- "igenomes_base": {
- "type": "string",
- "format": "directory-path",
- "description": "The base path to the igenomes reference files",
- "fa_icon": "fas fa-ban",
- "hidden": true,
- "default": "s3://ngi-igenomes/igenomes/"
- }
- }
- },
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
@@ -218,6 +179,12 @@
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
+ },
+ "trace_report_suffix": {
+ "type": "string",
+ "fa_icon": "far calendar",
+ "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
+ "hidden": true
}
}
}
@@ -226,9 +193,7 @@
{
"$ref": "#/$defs/input_output_options"
},
- {
- "$ref": "#/$defs/reference_genome_options"
- },
+
{
"$ref": "#/$defs/institutional_config_options"
},
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 00000000..69398a25
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,313 @@
+{
+ "@context": [
+ "https://w3id.org/ro/crate/1.1/context",
+ {
+ "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+ "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+ "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+ "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+ "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+ "TestService": "https://w3id.org/ro/terms/test#TestService",
+ "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+ "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+ "definition": "https://w3id.org/ro/terms/test#definition",
+ "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+ "instance": "https://w3id.org/ro/terms/test#instance",
+ "resource": "https://w3id.org/ro/terms/test#resource",
+ "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+ }
+ ],
+ "@graph": [
+ {
+ "@id": "./",
+ "@type": "Dataset",
+ "creativeWorkStatus": "InProgress",
+ "datePublished": "2024-12-12T11:24:56+00:00",
+ "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-viralrecon_logo_dark.png\">\n <img alt=\"nf-core/viralrecon\" src=\"docs/images/nf-core-viralrecon_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/viralrecon/actions/workflows/ci.yml)\n[](https://github.com/nf-core/viralrecon/actions/workflows/linting.yml)[](https://nf-co.re/viralrecon/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/viralrecon)\n\n[](https://nfcore.slack.com/channels/viralrecon)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/viralrecon** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/viralrecon \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/viralrecon/usage) and the [parameter documentation](https://nf-co.re/viralrecon/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/viralrecon/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/viralrecon/output).\n\n## Credits\n\nnf-core/viralrecon was originally written by Patel H, Varona S and Monzon S.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#viralrecon` channel](https://nfcore.slack.com/channels/viralrecon) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/viralrecon for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+ "hasPart": [
+ {
+ "@id": "main.nf"
+ },
+ {
+ "@id": "assets/"
+ },
+ {
+ "@id": "conf/"
+ },
+ {
+ "@id": "docs/"
+ },
+ {
+ "@id": "docs/images/"
+ },
+ {
+ "@id": "modules/"
+ },
+ {
+ "@id": "modules/nf-core/"
+ },
+ {
+ "@id": "workflows/"
+ },
+ {
+ "@id": "subworkflows/"
+ },
+ {
+ "@id": "nextflow.config"
+ },
+ {
+ "@id": "README.md"
+ },
+ {
+ "@id": "nextflow_schema.json"
+ },
+ {
+ "@id": "CHANGELOG.md"
+ },
+ {
+ "@id": "LICENSE"
+ },
+ {
+ "@id": "CODE_OF_CONDUCT.md"
+ },
+ {
+ "@id": "CITATIONS.md"
+ },
+ {
+ "@id": "modules.json"
+ },
+ {
+ "@id": "docs/usage.md"
+ },
+ {
+ "@id": "docs/output.md"
+ },
+ {
+ "@id": ".nf-core.yml"
+ },
+ {
+ "@id": ".pre-commit-config.yaml"
+ },
+ {
+ "@id": ".prettierignore"
+ }
+ ],
+ "isBasedOn": "https://github.com/nf-core/viralrecon",
+ "license": "MIT",
+ "mainEntity": {
+ "@id": "main.nf"
+ },
+ "mentions": [
+ {
+ "@id": "#8f645416-5238-4657-a672-7168ac446c69"
+ }
+ ],
+ "name": "nf-core/viralrecon"
+ },
+ {
+ "@id": "ro-crate-metadata.json",
+ "@type": "CreativeWork",
+ "about": {
+ "@id": "./"
+ },
+ "conformsTo": [
+ {
+ "@id": "https://w3id.org/ro/crate/1.1"
+ },
+ {
+ "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+ }
+ ]
+ },
+ {
+ "@id": "main.nf",
+ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+ "dateCreated": "",
+ "dateModified": "2024-12-12T11:24:56Z",
+ "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+ "keywords": [
+ "nf-core",
+ "nextflow",
+ "amplicon",
+ "artic",
+ "assembly",
+ "covid-19",
+ "covid19",
+ "illumina",
+ "long-read-sequencing",
+ "metagenomics",
+ "nanopore",
+ "ont",
+ "oxford-nanopore",
+ "sars-cov-2",
+ "variant-calling",
+ "viral",
+ "virus"
+ ],
+ "license": ["MIT"],
+ "name": ["nf-core/viralrecon"],
+ "programmingLanguage": {
+ "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+ },
+ "sdPublisher": {
+ "@id": "https://nf-co.re/"
+ },
+ "url": ["https://github.com/nf-core/viralrecon", "https://nf-co.re/viralrecon/dev/"],
+ "version": ["2.7.0dev"]
+ },
+ {
+ "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+ "@type": "ComputerLanguage",
+ "identifier": {
+ "@id": "https://www.nextflow.io/"
+ },
+ "name": "Nextflow",
+ "url": {
+ "@id": "https://www.nextflow.io/"
+ },
+ "version": "!>=24.04.2"
+ },
+ {
+ "@id": "#8f645416-5238-4657-a672-7168ac446c69",
+ "@type": "TestSuite",
+ "instance": [
+ {
+ "@id": "#67317226-37cb-4a6e-8606-0993a13ce69d"
+ }
+ ],
+ "mainEntity": {
+ "@id": "main.nf"
+ },
+ "name": "Test suite for nf-core/viralrecon"
+ },
+ {
+ "@id": "#67317226-37cb-4a6e-8606-0993a13ce69d",
+ "@type": "TestInstance",
+ "name": "GitHub Actions workflow for testing nf-core/viralrecon",
+ "resource": "repos/nf-core/viralrecon/actions/workflows/ci.yml",
+ "runsOn": {
+ "@id": "https://w3id.org/ro/terms/test#GithubService"
+ },
+ "url": "https://api.github.com"
+ },
+ {
+ "@id": "https://w3id.org/ro/terms/test#GithubService",
+ "@type": "TestService",
+ "name": "Github Actions",
+ "url": {
+ "@id": "https://github.com"
+ }
+ },
+ {
+ "@id": "assets/",
+ "@type": "Dataset",
+ "description": "Additional files"
+ },
+ {
+ "@id": "conf/",
+ "@type": "Dataset",
+ "description": "Configuration files"
+ },
+ {
+ "@id": "docs/",
+ "@type": "Dataset",
+ "description": "Markdown files for documenting the pipeline"
+ },
+ {
+ "@id": "docs/images/",
+ "@type": "Dataset",
+ "description": "Images for the documentation files"
+ },
+ {
+ "@id": "modules/",
+ "@type": "Dataset",
+ "description": "Modules used by the pipeline"
+ },
+ {
+ "@id": "modules/nf-core/",
+ "@type": "Dataset",
+ "description": "nf-core modules"
+ },
+ {
+ "@id": "workflows/",
+ "@type": "Dataset",
+ "description": "Main pipeline workflows to be executed in main.nf"
+ },
+ {
+ "@id": "subworkflows/",
+ "@type": "Dataset",
+ "description": "Smaller subworkflows"
+ },
+ {
+ "@id": "nextflow.config",
+ "@type": "File",
+ "description": "Main Nextflow configuration file"
+ },
+ {
+ "@id": "README.md",
+ "@type": "File",
+ "description": "Basic pipeline usage information"
+ },
+ {
+ "@id": "nextflow_schema.json",
+ "@type": "File",
+ "description": "JSON schema for pipeline parameter specification"
+ },
+ {
+ "@id": "CHANGELOG.md",
+ "@type": "File",
+ "description": "Information on changes made to the pipeline"
+ },
+ {
+ "@id": "LICENSE",
+ "@type": "File",
+ "description": "The license - should be MIT"
+ },
+ {
+ "@id": "CODE_OF_CONDUCT.md",
+ "@type": "File",
+ "description": "The nf-core code of conduct"
+ },
+ {
+ "@id": "CITATIONS.md",
+ "@type": "File",
+ "description": "Citations needed when using the pipeline"
+ },
+ {
+ "@id": "modules.json",
+ "@type": "File",
+ "description": "Version information for modules from nf-core/modules"
+ },
+ {
+ "@id": "docs/usage.md",
+ "@type": "File",
+ "description": "Usage documentation"
+ },
+ {
+ "@id": "docs/output.md",
+ "@type": "File",
+ "description": "Output documentation"
+ },
+ {
+ "@id": ".nf-core.yml",
+ "@type": "File",
+ "description": "nf-core configuration file, configuring template features and linting rules"
+ },
+ {
+ "@id": ".pre-commit-config.yaml",
+ "@type": "File",
+ "description": "Configuration file for pre-commit hooks"
+ },
+ {
+ "@id": ".prettierignore",
+ "@type": "File",
+ "description": "Ignore file for prettier"
+ },
+ {
+ "@id": "https://nf-co.re/",
+ "@type": "Organization",
+ "name": "nf-core",
+ "url": "https://nf-co.re/"
+ }
+ ]
+}
diff --git a/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf b/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
index 4bbe95ca..7563ed5f 100644
--- a/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
@@ -63,11 +63,6 @@ workflow PIPELINE_INITIALISATION {
nextflow_cli_args
)
- //
- // Custom validation for pipeline parameters
- //
- validateInputParameters()
-
//
// Create channel from input file provided through params.input
//
@@ -116,7 +111,8 @@ workflow PIPELINE_COMPLETION {
main:
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-
+ def multiqc_reports = multiqc_report.toList()
+
//
// Completion email and summary
//
@@ -129,7 +125,7 @@ workflow PIPELINE_COMPLETION {
plaintext_email,
outdir,
monochrome_logs,
- multiqc_report.toList()
+ multiqc_reports.getVal(),
)
}
@@ -149,12 +145,6 @@ workflow PIPELINE_COMPLETION {
FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-//
-// Check and validate pipeline parameters
-//
-def validateInputParameters() {
- genomeExistsError()
-}
//
// Validate channels from input samplesheet
@@ -171,31 +161,6 @@ def validateInputSamplesheet(input) {
return [ metas[0], fastqs ]
}
//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
- if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
- if (params.genomes[ params.genome ].containsKey(attribute)) {
- return params.genomes[ params.genome ][ attribute ]
- }
- }
- return null
-}
-
-//
-// Exit pipeline if incorrect --genome key provided
-//
-def genomeExistsError() {
- if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
- def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
- " Currently, the available genome keys are:\n" +
- " ${params.genomes.keySet().join(", ")}\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- error(error_string)
- }
-}
-//
// Generate methods description for MultiQC
//
def toolCitationText() {
@@ -225,7 +190,7 @@ def toolBibliographyText() {
}
def methodsDescriptionText(mqc_methods_yaml) {
- // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+ // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
def meta = [:]
meta.workflow = workflow.toMap()
meta["manifest_map"] = workflow.manifest.toMap()
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 0fcbf7b3..d6e593e8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -92,10 +92,12 @@ def checkCondaChannels() {
channels = config.channels
}
catch (NullPointerException e) {
+ log.debug(e)
log.warn("Could not verify conda channel configuration.")
return null
}
catch (IOException e) {
+ log.debug(e)
log.warn("Could not verify conda channel configuration.")
return null
}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
}
then {
- assertAll(
- { assert workflow.success },
- { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
- )
+ expect {
+ with(workflow) {
+ assert success
+ assert "nextflow_workflow v9.9.9" in stdout
+ }
+ }
}
}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5cb7bafe..bfd25876 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) {
}
}
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
- def temp_doi_ref = ""
- def manifest_doi = workflow.manifest.doi.tokenize(",")
- // Handling multiple DOIs
- // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
- // Removing ` ` since the manifest.doi is a string and not a proper list
- manifest_doi.each { doi_ref ->
- temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
- }
- return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
//
// Generate workflow version string
//
@@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) {
return yaml_file_text
}
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
- def colors = logColours(monochrome_logs) as Map
- String.format(
- """\n
- ${dashedLine(monochrome_logs)}
- ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
- ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
- ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
- ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset}
- ${colors.green}`._,._,\'${colors.reset}
- ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
- ${dashedLine(monochrome_logs)}
- """.stripIndent()
- )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
- def colors = logColours(monochrome_logs) as Map
- return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
//
// ANSII colours used for terminal logging
//
@@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) {
return colorcodes
}
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
- def mqc_report = null
- try {
- if (workflow.success) {
- mqc_report = multiqc_report.getVal()
- if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
- if (mqc_report.size() > 1) {
- log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
- }
- mqc_report = mqc_report[0]
- }
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+ if (multiqc_reports instanceof Path) {
+ return multiqc_reports
+ } else if (multiqc_reports instanceof List) {
+ if (multiqc_reports.size() == 0) {
+ log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+ return null
+ } else if (multiqc_reports.size() == 1) {
+ return multiqc_reports.first()
+ } else {
+ log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+ return multiqc_reports.first()
}
+ } else {
+ return null
}
- catch (Exception all) {
- if (multiqc_report) {
- log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
- }
- }
- return mqc_report
}
//
@@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
email_fields['summary'] = summary << misc_fields
// On success try attach the multiqc report
- def mqc_report = attachMultiqcReport(multiqc_report)
+ def mqc_report = getSingleReport(multiqc_report)
// Check if we are only sending emails on failure
def email_address = email
@@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
def email_html = html_template.toString()
// Render the sendmail template
- def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+ def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
@@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
if (email_address) {
try {
if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+ new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+ }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
['sendmail', '-t'].execute() << sendmail_html
log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
}
- catch (Exception all) {
+ catch (Exception msg) {
+ log.debug(msg.toString())
+ log.debug("Trying with mail instead of sendmail")
// Catch failures and try with plaintext
def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
mail_cmd.execute() << email_html
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f8..f117040c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
}
}
- test("Test Function workflowCitation") {
-
- function "workflowCitation"
-
- then {
- assertAll(
- { assert function.success },
- { assert snapshot(function.result).match() }
- )
- }
- }
-
- test("Test Function nfCoreLogo") {
+ test("Test Function without logColours") {
- function "nfCoreLogo"
+ function "logColours"
when {
function {
"""
- input[0] = false
+ input[0] = true
"""
}
}
@@ -73,9 +61,8 @@ nextflow_function {
}
}
- test("Test Function dashedLine") {
-
- function "dashedLine"
+ test("Test Function with logColours") {
+ function "logColours"
when {
function {
@@ -93,14 +80,13 @@ nextflow_function {
}
}
- test("Test Function without logColours") {
-
- function "logColours"
+ test("Test Function getSingleReport with a single file") {
+ function "getSingleReport"
when {
function {
"""
- input[0] = true
+ input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
"""
}
}
@@ -108,18 +94,22 @@ nextflow_function {
then {
assertAll(
{ assert function.success },
- { assert snapshot(function.result).match() }
+ { assert function.result.contains("test.tsv") }
)
}
}
- test("Test Function with logColours") {
- function "logColours"
+ test("Test Function getSingleReport with multiple files") {
+ function "getSingleReport"
when {
function {
"""
- input[0] = false
+ input[0] = [
+ file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+ file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+ file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+ ]
"""
}
}
@@ -127,7 +117,9 @@ nextflow_function {
then {
assertAll(
{ assert function.success },
- { assert snapshot(function.result).match() }
+ { assert function.result.contains("test.tsv") },
+ { assert !function.result.contains("network.tsv") },
+ { assert !function.result.contains("expression.tsv") }
)
}
}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232c..02c67014 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
},
"timestamp": "2024-02-28T12:02:59.729647"
},
- "Test Function nfCoreLogo": {
- "content": [
- "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-28T12:03:10.562934"
- },
- "Test Function workflowCitation": {
- "content": [
- "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-28T12:03:07.019761"
- },
"Test Function without logColours": {
"content": [
{
@@ -95,16 +75,6 @@
},
"timestamp": "2024-02-28T12:03:17.969323"
},
- "Test Function dashedLine": {
- "content": [
- "-\u001b[2m----------------------------------------------------\u001b[0m-"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-28T12:03:14.366181"
- },
"Test Function with logColours": {
"content": [
{
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc432..8fb30164 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
params {
test_data = ''
- outdir = 1
+ outdir = null
}
workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
params {
test_data = ''
- outdir = 1
+ outdir = null
}
workflow {
diff --git a/workflows/viralrecon.nf b/workflows/viralrecon.nf
index 7ea56421..2b4ce0ad 100644
--- a/workflows/viralrecon.nf
+++ b/workflows/viralrecon.nf
@@ -39,7 +39,7 @@ workflow VIRALRECON {
softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
- name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml',
+ name: 'nf_core_' + 'viralrecon_software_' + 'mqc_' + 'versions.yml',
sort: true,
newLine: true
).set { ch_collated_versions }
From 03661d5a5de4ed82f2c0b1badbc3c4d26f214745 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 20 Dec 2024 13:11:00 +0000
Subject: [PATCH 2/3] Template update for nf-core/tools version 3.1.1
---
.editorconfig | 4 ++
.github/ISSUE_TEMPLATE/bug_report.yml | 1 -
.github/workflows/download_pipeline.yml | 41 +++++++++++--------
.nf-core.yml | 2 +-
.prettierignore | 1 +
CITATIONS.md | 4 +-
LICENSE | 2 +-
README.md | 15 ++-----
docs/output.md | 11 ++---
docs/usage.md | 2 +-
nextflow.config | 3 ++
nextflow_schema.json | 1 -
ro-crate-metadata.json | 39 ++++++++++++------
.../utils_nfcore_viralrecon_pipeline/main.nf | 2 +-
14 files changed, 71 insertions(+), 57 deletions(-)
diff --git a/.editorconfig b/.editorconfig
index 72dda289..6d9b74cc 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
# ignore python and markdown
[*.{py,md}]
indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 06642ab6..40f83f55 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,7 +9,6 @@ body:
- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [nf-core/viralrecon pipeline documentation](https://nf-co.re/viralrecon/usage)
-
- type: textarea
id: description
attributes:
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2576cc0c..13b51e2c 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -28,8 +28,12 @@ env:
NXF_ANSI_LOG: false
jobs:
- download:
+ configure:
runs-on: ubuntu-latest
+ outputs:
+ REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+ REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+ REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
@@ -53,22 +57,27 @@ jobs:
pip install git+https://github.com/nf-core/tools.git@dev
- name: Get the repository name and current branch set as environment variable
+ id: get_repo_properties
run: |
- echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
- echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
- echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+ echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+ echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+ echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
- name: Make a cache directory for the container images
run: |
mkdir -p ./singularity_container_images
+ download:
+ runs-on: ubuntu-latest
+ needs: configure
+ steps:
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
run: |
- nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
- --revision ${{ env.REPO_BRANCH }} \
- --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+ nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+ --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+ --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
--compress "none" \
--container-system 'singularity' \
--container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
@@ -76,14 +85,14 @@ jobs:
--download-configuration 'yes'
- name: Inspect download
- run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+ run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
- name: Count the downloaded number of container images
id: count_initial
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Initial container image count: $image_count"
- echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+ echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
@@ -91,27 +100,27 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
- run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+ run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
- if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+ if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
- run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+ run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
- name: Count the downloaded number of container images
id: count_afterwards
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Post-pipeline run container image count: $image_count"
- echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+ echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
- name: Compare container image counts
run: |
- if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
- initial_count=${{ env.IMAGE_COUNT_INITIAL }}
- final_count=${{ env.IMAGE_COUNT_AFTER }}
+ if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+ initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+ final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
difference=$((final_count - initial_count))
echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
tree ./singularity_container_images
diff --git a/.nf-core.yml b/.nf-core.yml
index cd2763f2..6032c967 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,7 +2,7 @@ lint:
files_unchanged:
- assets/email_template.html
- assets/email_template.txt
-nf_core_version: 3.1.0
+nf_core_version: 3.1.1
repository_type: pipeline
template:
author: Patel H, Varona S and Monzon S
diff --git a/.prettierignore b/.prettierignore
index 437d763d..edd29f01 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,3 +10,4 @@ testing/
testing*
*.pyc
bin/
+ro-crate-metadata.json
diff --git a/CITATIONS.md b/CITATIONS.md
index 8d5f2e68..c587f552 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,9 +12,7 @@
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [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.
diff --git a/LICENSE b/LICENSE
index 8f37c353..cd1a3af0 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT License
-Copyright (c) Patel H, Varona S and Monzon S
+Copyright (c) The nf-core/viralrecon team
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 80f33ba0..1036879d 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,7 @@
<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-viralrecon_logo_dark.png">
<img alt="nf-core/viralrecon" src="docs/images/nf-core-viralrecon_logo_light.png">
</picture>
-</h1>
-
-[](https://github.com/nf-core/viralrecon/actions/workflows/ci.yml)
+</h1>[](https://github.com/nf-core/viralrecon/actions/workflows/ci.yml)
[](https://github.com/nf-core/viralrecon/actions/workflows/linting.yml)[](https://nf-co.re/viralrecon/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
[](https://www.nf-test.com)
@@ -29,15 +27,12 @@
<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
## Usage
> [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -94,9 +89,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations
<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/viralrecon 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 -->
+<!-- If you use nf-core/viralrecon 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.
diff --git a/docs/output.md b/docs/output.md
index 3cd8d227..77d21856 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -12,8 +12,7 @@ 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
+- [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
@@ -27,9 +26,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
</details>
-[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/).
-
-### MultiQC
+[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/).### MultiQC
<details markdown="1">
<summary>Output files</summary>
@@ -43,9 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-
-### Pipeline information
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.### Pipeline information
<details markdown="1">
<summary>Output files</summary>
diff --git a/docs/usage.md b/docs/usage.md
index f5fb5239..ad5581bb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -129,7 +129,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli
> [!IMPORTANT]
> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
They are loaded in sequence, so later profiles can overwrite earlier profiles.
diff --git a/nextflow.config b/nextflow.config
index 897dcdf2..93d642e3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -285,3 +285,6 @@ validation {
afterText = validation.help.afterText
}
}
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5fbb6cc5..6320120e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -193,7 +193,6 @@
{
"$ref": "#/$defs/input_output_options"
},
-
{
"$ref": "#/$defs/institutional_config_options"
},
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 69398a25..1289a133 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
- "datePublished": "2024-12-12T11:24:56+00:00",
- "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-viralrecon_logo_dark.png\">\n <img alt=\"nf-core/viralrecon\" src=\"docs/images/nf-core-viralrecon_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/viralrecon/actions/workflows/ci.yml)\n[](https://github.com/nf-core/viralrecon/actions/workflows/linting.yml)[](https://nf-co.re/viralrecon/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/viralrecon)\n\n[](https://nfcore.slack.com/channels/viralrecon)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/viralrecon** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/viralrecon \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/viralrecon/usage) and the [parameter documentation](https://nf-co.re/viralrecon/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/viralrecon/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/viralrecon/output).\n\n## Credits\n\nnf-core/viralrecon was originally written by Patel H, Varona S and Monzon S.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#viralrecon` channel](https://nfcore.slack.com/channels/viralrecon) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/viralrecon for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+ "datePublished": "2024-12-20T13:10:59+00:00",
+ "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-viralrecon_logo_dark.png\">\n <img alt=\"nf-core/viralrecon\" src=\"docs/images/nf-core-viralrecon_logo_light.png\">\n </picture>\n</h1>[](https://github.com/nf-core/viralrecon/actions/workflows/ci.yml)\n[](https://github.com/nf-core/viralrecon/actions/workflows/linting.yml)[](https://nf-co.re/viralrecon/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/viralrecon)\n\n[](https://nfcore.slack.com/channels/viralrecon)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/viralrecon** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/viralrecon \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/viralrecon/usage) and the [parameter documentation](https://nf-co.re/viralrecon/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/viralrecon/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/viralrecon/output).\n\n## Credits\n\nnf-core/viralrecon was originally written by Patel H, Varona S and Monzon S.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#viralrecon` channel](https://nfcore.slack.com/channels/viralrecon) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/viralrecon 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 -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
"hasPart": [
{
"@id": "main.nf"
@@ -99,7 +99,7 @@
},
"mentions": [
{
- "@id": "#8f645416-5238-4657-a672-7168ac446c69"
+ "@id": "#35caead0-4680-4fa7-8f9a-5c5cf6084396"
}
],
"name": "nf-core/viralrecon"
@@ -121,9 +121,13 @@
},
{
"@id": "main.nf",
- "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+ "@type": [
+ "File",
+ "SoftwareSourceCode",
+ "ComputationalWorkflow"
+ ],
"dateCreated": "",
- "dateModified": "2024-12-12T11:24:56Z",
+ "dateModified": "2024-12-20T13:10:59Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nf-core",
@@ -144,16 +148,25 @@
"viral",
"virus"
],
- "license": ["MIT"],
- "name": ["nf-core/viralrecon"],
+ "license": [
+ "MIT"
+ ],
+ "name": [
+ "nf-core/viralrecon"
+ ],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
},
"sdPublisher": {
"@id": "https://nf-co.re/"
},
- "url": ["https://github.com/nf-core/viralrecon", "https://nf-co.re/viralrecon/dev/"],
- "version": ["2.7.0dev"]
+ "url": [
+ "https://github.com/nf-core/viralrecon",
+ "https://nf-co.re/viralrecon/dev/"
+ ],
+ "version": [
+ "2.7.0dev"
+ ]
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -168,11 +181,11 @@
"version": "!>=24.04.2"
},
{
- "@id": "#8f645416-5238-4657-a672-7168ac446c69",
+ "@id": "#35caead0-4680-4fa7-8f9a-5c5cf6084396",
"@type": "TestSuite",
"instance": [
{
- "@id": "#67317226-37cb-4a6e-8606-0993a13ce69d"
+ "@id": "#3578dad2-91b1-47e7-adf3-e43ef842f7ca"
}
],
"mainEntity": {
@@ -181,7 +194,7 @@
"name": "Test suite for nf-core/viralrecon"
},
{
- "@id": "#67317226-37cb-4a6e-8606-0993a13ce69d",
+ "@id": "#3578dad2-91b1-47e7-adf3-e43ef842f7ca",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/viralrecon",
"resource": "repos/nf-core/viralrecon/actions/workflows/ci.yml",
@@ -310,4 +323,4 @@
"url": "https://nf-co.re/"
}
]
-}
+}
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf b/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
index 7563ed5f..b4335879 100644
--- a/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_viralrecon_pipeline/main.nf
@@ -112,7 +112,7 @@ workflow PIPELINE_COMPLETION {
main:
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
def multiqc_reports = multiqc_report.toList()
-
+
//
// Completion email and summary
//
From 1864f1d64a7931fb6fd628ee2901dde0f16f5177 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Mon, 30 Dec 2024 17:00:44 -0600
Subject: [PATCH 3/3] Empty commit after updating base to dev
---
main.nf | 2 --
1 file changed, 2 deletions(-)
diff --git a/main.nf b/main.nf
index 2be98534..e785997d 100644
--- a/main.nf
+++ b/main.nf
@@ -35,7 +35,6 @@ params.nextclade_dataset = getGenomeAttribute('nextclade_dataset_v3pl'
params.nextclade_dataset_name = getGenomeAttribute('nextclade_dataset_name')
params.nextclade_dataset_tag = getGenomeAttribute('nextclade_dataset_tag_v3pl')
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -48,7 +47,6 @@ if (params.platform == 'illumina') {
include { NANOPORE } from './workflows/nanopore'
}
-include { VIRALRECON } from './workflows/viralrecon'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_viralrecon_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_viralrecon_pipeline'