diff --git a/.editorconfig b/.editorconfig
index b78de6e655d209990fd9c1e70ae4882a9f0b4dff..b6b3190776e8d7f8894ed6484494018355814fc6 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2
# These files are edited and tested upstream in nf-core/modules
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index e405327c328cc2a94ebadf33e9ac4cad766f7461..eb120e620804963a925960001d73a8e3bd777e8e 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -45,6 +45,6 @@ body:
* Nextflow version _(eg. 22.10.1)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
- * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of nf-core/hic _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index c67458d182e840707cbccc6914ff1e3d95331b0e..e2cdeccdb74daad910d876e4ed48f987e3b6c2a4 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c528fffcb40acc23443d90b0eb8f0922cfb265f2..014f094c61261d53c41ebe43d9a6c3e786d6a3bb 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
- uses: nf-core/tower-action@v3
+ uses: seqeralabs/action-tower-launch@v1
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 3f9b365ffe5729722f94316715fe5e654860c152..e7311630f36239a1b58fd7a88c3dd1a07c2f2ea6 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
- uses: nf-core/tower-action@v3
+ uses: seqeralabs/action-tower-launch@v1
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index b92e3d24195d72e7a4c39605fd29de3cf657bd06..edf46df1d97b83fde71552d4d7bec5577962f318 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/hic'
run: |
- { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+ { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
new file mode 100644
index 0000000000000000000000000000000000000000..694e90ecb1c9135ea3d776cc01b197755c1aa040
--- /dev/null
+++ b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+ schedule:
+ - cron: "0 0 * * 0" # Once a week
+
+jobs:
+ clean-up:
+ runs-on: ubuntu-latest
+ permissions:
+ issues: write
+ pull-requests: write
+ steps:
+ - uses: actions/stale@v7
+ with:
+ stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+ stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+ close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+ days-before-stale: 30
+ days-before-close: 20
+ days-before-pr-close: -1
+ any-of-labels: "awaiting-changes,awaiting-feedback"
+ exempt-issue-labels: "WIP"
+ exempt-pr-labels: "WIP"
+ repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 858d622efc884fba438eb48c80d4122443dfa3a0..888cb4bc35cedc7a372ba1056495d9ee7a4a4bb7 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -78,7 +78,7 @@ jobs:
- uses: actions/setup-python@v4
with:
- python-version: "3.7"
+ python-version: "3.8"
architecture: "x64"
- name: Install dependencies
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0c31cdb99ffe569deddbf0ef78e9e5962073d158
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+ - repo: https://github.com/pre-commit/mirrors-prettier
+ rev: "v2.7.1"
+ hooks:
+ - id: prettier
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1b0b90bd8bd3900aff3776755dc35f342210efd4..3a475fb42f5c0962af397e653120a04587c818c9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v1.4.0dev - [date]
+## v2.1.0dev - [date]
Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
index b2c63a1ffc96f8aa3329efcbdca6f2c2cef1e69d..354b9804d3eb5745618f047420de1c45f62068d4 100644
--- a/README.md
+++ b/README.md
@@ -8,57 +8,71 @@
[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/hic)
-[](https://nfcore.slack.com/channels/hic)[](https://twitter.com/nf_core)[](https://www.youtube.com/c/nf-core)
+[](https://nfcore.slack.com/channels/hic)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
-<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
+**nf-core/hic** is a bioinformatics pipeline that ...
-**nf-core/hic** is a bioinformatics best-practice analysis pipeline for Analysis of Chromosome Conformation Capture data (Hi-C).
-
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
-
-<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
-
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
-
-## Pipeline summary
+<!-- TODO nf-core:
+ Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
+ major pipeline sections and the types of output it produces. You're giving an overview to someone new
+ to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
+-->
+<!-- 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/))
-## Quick Start
+## 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.
+
+<!-- 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):
+
+First, prepare a samplesheet with your input data that looks as follows:
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+`samplesheet.csv`:
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
+```csv
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+```
-3. Download the pipeline and test it on a minimal dataset with a single command:
+Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
- ```bash
- nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
- ```
+-->
- Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+Now, you can run the pipeline using:
- > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
- > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
- > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
- > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-4. Start running your own analysis!
+```bash
+nextflow run nf-core/hic \
+ -profile <docker/singularity/.../institute> \
+ --input samplesheet.csv \
+ --outdir <OUTDIR>
+```
- <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+> **Warning:**
+> 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/usage/configuration#custom-configuration-files).
- ```bash
- nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
- ```
+For more details, please refer to the [usage documentation](https://nf-co.re/hic/usage) and the [parameter documentation](https://nf-co.re/hic/parameters).
-## Documentation
+## Pipeline output
-The nf-core/hic pipeline comes with documentation about the pipeline [usage](https://nf-co.re/hic/usage), [parameters](https://nf-co.re/hic/parameters) and [output](https://nf-co.re/hic/output).
+To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/hic/results) tab on the nf-core website pipeline page.
+For more details about the output files and reports, please refer to the
+[output documentation](https://nf-co.re/hic/output).
## Credits
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 11b155723a63c779ccde1ef268de82a0553e5a84..4a758fe0036e6de4ce523890164d21ecbbfc56aa 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -158,9 +158,6 @@ def sniff_format(handle):
peek = read_head(handle)
handle.seek(0)
sniffer = csv.Sniffer()
- if not sniffer.has_header(peek):
- logger.critical("The given sample sheet does not appear to contain a header.")
- sys.exit(1)
dialect = sniffer.sniff(peek)
return dialect
diff --git a/conf/base.config b/conf/base.config
index 66977ffb4f505a876f501f827b5d3d2c2b44f337..74a33d164184236fcd78197fc390efb6725a69b1 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
- errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+ errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 7a1b3ac6d3a3d6c4ec0af72f7879f4958cf35621..3f1143775951af7fd2177938efd9445fa3db2f67 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -36,6 +36,14 @@ params {
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/"
diff --git a/conf/test_full.config b/conf/test_full.config
index 7c09bad68736cdc576acdcae05cc56753b182a5a..4c22dc27b8ca7583a09a997f01d0d833c43ee828 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -10,6 +10,8 @@
----------------------------------------------------------------------------------------
*/
+cleanup = true
+
params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'
diff --git a/docs/usage.md b/docs/usage.md
index e0dab28a5e3b6e3b06d599b7009ce054c99fb76f..506b575a76a33e73e05b68a5ce33d70c4ceec773 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -71,6 +71,29 @@ work # Directory containing the nextflow working files
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```
+If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
+
+Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
+
+> ⚠️ 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:
+
+```bash
+nextflow run nf-core/hic -profile docker -params-file params.yaml
+```
+
+with `params.yaml` containing:
+
+```yaml
+input: './samplesheet.csv'
+outdir: './results/'
+genome: 'GRCh37'
+input: 'data'
+<...>
+```
+
+You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
+
### Updating the pipeline
When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
@@ -87,6 +110,10 @@ First, go to the [nf-core/hic releases page](https://github.com/nf-core/hic/rele
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.
+
+> 💡 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
> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
@@ -95,7 +122,7 @@ This version number will be logged in reports when you run the pipeline, so that
Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
-Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below.
+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.
> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
@@ -119,8 +146,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
- `charliecloud`
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+- `apptainer`
+ - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `conda`
- - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
+ - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
### `-resume`
@@ -138,102 +167,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
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.
-For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue:
-
-```console
-[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
-Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
-
-Caused by:
- Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
-
-Command executed:
- STAR \
- --genomeDir star \
- --readFilesIn WT_REP1_trimmed.fq.gz \
- --runThreadN 2 \
- --outFileNamePrefix WT_REP1. \
- <TRUNCATED>
-
-Command exit status:
- 137
-
-Command output:
- (empty)
-
-Command error:
- .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. <TRUNCATED>
-Work dir:
- /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb
-
-Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-```
-
-#### For beginners
-
-A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.
-
-#### Advanced option on process level
-
-To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`.
-If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
-The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
-The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
-Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB.
-The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
-
-```nextflow
-process {
- withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
- memory = 100.GB
- }
-}
-```
-
-> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
->
-> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
-
-### Updating containers (advanced users)
-
-The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
-
-1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19)
-2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
-3. Create the custom config accordingly:
-
- - For Docker:
+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.
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
+### Custom Containers
- - For Singularity:
+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.
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
+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.
- - For Conda:
+### Custom Tool Arguments
- ```nextflow
- process {
- withName: PANGOLIN {
- conda = 'bioconda::pangolin=3.0.5'
- }
- }
- ```
+A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
-> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
### nf-core/configs
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index 33cd4f6e8df62276afa55ab4c00cd59900ea013e..9b34804d6dfd27ce0c723125a9875e23671e4c4a 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -2,6 +2,7 @@
// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
//
+import nextflow.Nextflow
import org.everit.json.schema.Schema
import org.everit.json.schema.loader.SchemaLoader
import org.everit.json.schema.ValidationException
@@ -83,6 +84,7 @@ class NfcoreSchema {
'stub-run',
'test',
'w',
+ 'with-apptainer',
'with-charliecloud',
'with-conda',
'with-dag',
@@ -177,7 +179,7 @@ class NfcoreSchema {
}
if (has_error) {
- System.exit(1)
+ Nextflow.error('Exiting!')
}
}
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index 71742bd90a12a1b6aa0a4e77102684d0ccd0366f..e51a467a6c8bebfb8ca4c605451d73afcb80c821 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -2,6 +2,7 @@
// This file holds several functions specific to the workflow/hic.nf in the nf-core/hic pipeline
//
+import nextflow.Nextflow
import groovy.text.SimpleTemplateEngine
class WorkflowHic {
@@ -14,8 +15,7 @@ class WorkflowHic {
if (!params.fasta) {
- log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
- System.exit(1)
+ Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
}
}
@@ -61,17 +61,19 @@ class WorkflowHic {
def description_html = engine.createTemplate(methods_text).make(meta)
return description_html
- }//
+ }
+
+ //
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
- log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+ 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" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- System.exit(1)
+ Nextflow.error(error_string)
}
}
}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index dd0c03d0324ab3919ef3e3389662d3cee83cd59d..978ce773b7b2536afd1525f678e360a7e4336ea6 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -2,6 +2,8 @@
// This file holds several functions specific to the main.nf workflow in the nf-core/hic pipeline
//
+import nextflow.Nextflow
+
class WorkflowMain {
//
@@ -21,7 +23,7 @@ class WorkflowMain {
//
// Generate help string
//
- public static String help(workflow, params, log) {
+ public static String help(workflow, params) {
def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
def help_string = ''
help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
@@ -34,7 +36,7 @@ class WorkflowMain {
//
// Generate parameter summary log string
//
- public static String paramsSummaryLog(workflow, params, log) {
+ public static String paramsSummaryLog(workflow, params) {
def summary_log = ''
summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
@@ -49,7 +51,7 @@ class WorkflowMain {
public static void initialise(workflow, params, log) {
// Print help to screen if required
if (params.help) {
- log.info help(workflow, params, log)
+ log.info help(workflow, params)
System.exit(0)
}
@@ -61,7 +63,7 @@ class WorkflowMain {
}
// Print parameter summary log to screen
- log.info paramsSummaryLog(workflow, params, log)
+ log.info paramsSummaryLog(workflow, params)
// Validate workflow parameters via the JSON schema
if (params.validate_params) {
@@ -81,8 +83,7 @@ class WorkflowMain {
// Check input has been provided
if (!params.input) {
- log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
- System.exit(1)
+ Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
}
}
//
diff --git a/main.nf b/main.nf
index d8cba4a8254ba1a3d56f937c17123ed419433a2d..7dd9be5444a4e18d22ff2c8215f7038b167062a0 100644
--- a/main.nf
+++ b/main.nf
@@ -4,7 +4,6 @@
nf-core/hic
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/hic
-
Website: https://nf-co.re/hic
Slack : https://nfcore.slack.com/channels/hic
----------------------------------------------------------------------------------------
diff --git a/modules.json b/modules.json
index 4297c820a7902b53557a0d6be5e2b40e9f7c11f4..072b219c4dec46f9322b00995de681988dceef6c 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
"nf-core": {
"custom/dumpsoftwareversions": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"installed_by": ["modules"]
},
"fastqc": {
@@ -17,7 +17,7 @@
},
"multiqc": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"installed_by": ["modules"]
}
}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 1624dfafe6425f07bbd15daf3b2735ea1187c0ec..096c80b0bd37b9a40bbf61cdefa13007f58b0c5d 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
- 'quay.io/biocontainers/python:3.8.3' }"
+ 'biocontainers/python:3.8.3' }"
input:
path samplesheet
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df21765b90921413962c3bb5ca44d117d829297..800a60991a3fc2da7acf5211b7d2d05a3b3fbdc2 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
label 'process_single'
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
index 60b546a012c457b5459490e732e6ac9be6979db1..c32657de7a2c09e82da1e753a234300fb76237ed 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: custom_dumpsoftwareversions
description: Custom module used to dump software versions within the nf-core pipeline template
keywords:
- custom
+ - dump
- version
tools:
- custom:
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 68f66bea74a65319549b9834af05cc9a38a1f30a..4b604749f5adef79787ae5802881109b9695e8fc 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_single'
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ebc29b279d565eb11d8923de0b87fd2fb14b1cbe..f93b5ee51907e991cb10045f5355a4552a27db40 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: MultiQC
description: Aggregate results from bioinformatics analyses across many samples into a single report
keywords:
@@ -37,7 +38,7 @@ output:
description: MultiQC report file
pattern: "multiqc_report.html"
- data:
- type: dir
+ type: directory
description: MultiQC data dir
pattern: "multiqc_data"
- plots:
diff --git a/nextflow.config b/nextflow.config
index dacdcf068871a9702876f466b820fb6b6d186896..b1f98b3463e5516a12e44e2dca75c58b0058e4dc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -78,7 +78,11 @@ try {
profiles {
- debug { process.beforeScript = 'echo $HOSTNAME' }
+ debug {
+ dumpHashes = true
+ process.beforeScript = 'echo $HOSTNAME'
+ cleanup = false
+ }
conda {
conda.enabled = true
docker.enabled = false
@@ -86,6 +90,7 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
mamba {
conda.enabled = true
@@ -95,14 +100,18 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
docker {
docker.enabled = true
+ docker.registry = 'quay.io'
docker.userEmulation = true
+ conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -110,31 +119,49 @@ profiles {
singularity {
singularity.enabled = true
singularity.autoMounts = true
+ conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
podman {
podman.enabled = true
+ podman.registry = 'quay.io'
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
shifter {
shifter.enabled = true
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
+ apptainer.enabled = false
+ }
+ apptainer {
+ apptainer.enabled = true
+ conda.enabled = false
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
@@ -193,7 +220,7 @@ manifest {
description = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
- version = '1.4.0dev'
+ version = '2.1.0dev'
doi = ''
}
diff --git a/tower.yml b/tower.yml
new file mode 100644
index 0000000000000000000000000000000000000000..787aedfe920c803b6733a8c8a8bafd585e73a264
--- /dev/null
+++ b/tower.yml
@@ -0,0 +1,5 @@
+reports:
+ multiqc_report.html:
+ display: "MultiQC HTML report"
+ samplesheet.csv:
+ display: "Auto-created samplesheet with collated metadata and FASTQ paths"