diff --git a/.editorconfig b/.editorconfig
index 75c2fe61f4886762396871469bba8684f282add2..43c7138733277a83ffc7e788e0283df17f6ccf71 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/awstest.yml b/.github/workflows/awstest.yml
index 177543c03385b4a9528124d6fb2ee6b995f6ac33..23c4973be1dea45f100e25c3f1b66486274b7f56 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/README.md b/README.md
index 973e1321c8c96f11bf6c704ca4372aea401cb8ac..df0a41991f3629fae502e434a2bdfbc46e115e57 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@
[](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
@@ -36,34 +36,45 @@ On release, automated continuous integration tests run the pipeline on a full-si
8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
9. Quality control report ([`MultiQC`](https://multiqc.info/))
-## Quick Start
+## Usage
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+> **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.
-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))_.
+First, prepare a samplesheet with your input data that looks as follows:
-3. Download the pipeline and test it on a minimal dataset with a single command:
+`samplesheet.csv`:
- ```bash
- nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
- ```
+```csv
+sample,fastq_1,fastq_2
+HIC_ES_4,SRR5339783_1.fastq.gz,SRR5339783_2.fastq.gz
+```
- 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.
+Each row represents a pair of fastq files (paired end).
+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.
+```bash
+nextflow run nf-core/hic \
+ -profile <docker/singularity/.../institute> \
+ --input samplesheet.csv \
+ --genome GRCh37 \
+ --outdir <OUTDIR>
+```
-4. Start running your own analysis!
+> **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 c498ef45ee96e33a8d4f81b0be948028c712db61..dde3baaa26969f03313e3d6070633770def3c738 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -157,9 +157,6 @@ 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 6808dbe2205a3cbe53975d4d2d2ec2fbc1998ec7..2558cb1be3b55fa76fac6e98671f945093579d44 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,7 +14,7 @@ process {
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.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 8b49d0827c7f45bb7f874427d7210c7f1eda3421..f4c32e3ac16734e10fe6da91f4467b0cbb39198e 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -19,6 +19,14 @@ params {
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
}
+ '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 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
diff --git a/conf/test_full.config b/conf/test_full.config
index f7b39d4fe2c22e98608b0ce00dec75274bde30ca..0a3a68ff20677cea809b7d9f38dbe9976e885395 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -9,6 +9,8 @@
----------------------------------------------------------------------------------------
*/
+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 961766cbf434073443c9147dd4afee2ef8aa6fcb..4ad48da5087a541195d98f097c625aa22b5a6062 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -64,6 +64,29 @@ 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>`.
+
+> âš ï¸ 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:
@@ -80,6 +103,10 @@ 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
@@ -90,7 +117,7 @@ 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.
@@ -123,8 +150,10 @@ 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`
@@ -144,102 +173,19 @@ for more information.
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 3dea732db2bb9c05d5002920297d8d727efea9d0..f14c26c5b91565eeca44afa6d51e3442e213bf16 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 {
@@ -14,14 +15,12 @@ class WorkflowHic {
// digestion parameters
if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
- log.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
- System.exit(1)
+ Nextflow.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
}
// Check Digestion or DNase Hi-C mode
//if (!params.dnase && !params.ligation_site) {
- // log.error "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
- // System.exit(1)
+ // Nextflow.error "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
//}
}
@@ -68,17 +67,19 @@ class WorkflowHic {
def description_html = engine.createTemplate(methods_text).make(meta)
return description_html
- }//
+ }
+
+ //
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
- log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+ def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" Genome '${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 239d4fe7253d3a060bd99bff6b7842cdeb2891c8..e4bce38300fadf0f573d90304d0ae40606327a3a 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 {
//
@@ -20,7 +22,7 @@ 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)
@@ -33,7 +35,7 @@ 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)
@@ -48,7 +50,7 @@ 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)
}
@@ -60,7 +62,7 @@ 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) {
@@ -80,8 +82,7 @@ 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 dd564aa4e80652c1a21ba504c0564faddfb74bcd..82aaf0f200b77db6710472f821c715376d2e5668 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/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index 34b27aab498c8e1c45355d01b991d5900a619f33..271913ec49b1d362b6b0fb065506961d85ad82fc 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -1,27 +1,27 @@
process BUILD_CONTACT_MAPS{
- tag "${meta.id}"
- label 'process_high_memory'
+ tag "${meta.id}"
+ label 'process_high_memory'
- conda "conda-forge::sed=4.7"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'quay.io/nf-core/ubuntu:20.04' }"
+ conda "conda-forge::sed=4.7"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+ 'nf-core/ubuntu:20.04' }"
- input:
- tuple val(meta), path(vpairs), val(resolution)
- tuple val(meta2), path(chrsize)
+ input:
+ tuple val(meta), path(vpairs), val(resolution)
+ tuple val(meta2), path(chrsize)
- output:
- tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
+ output:
+ tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
- script:
- def prefix = task.ext.prefix ?: "${meta.id}"
- """
- build_matrix \\
- --matrix-format upper \\
- --binsize ${resolution} \\
- --chrsizes ${chrsize} \\
- --ifile ${vpairs} \\
- --oprefix ${prefix}
- """
+ script:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ build_matrix \\
+ --matrix-format upper \\
+ --binsize ${resolution} \\
+ --chrsizes ${chrsize} \\
+ --ifile ${vpairs} \\
+ --oprefix ${prefix}
+ """
}
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 25c437ef795882591b0f50fcf4a235f29dc60822..2dcb63d176704a97fcb87fa3cf391f6ec9f5888d 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'quay.io/nf-core/ubuntu:20.04' }"
+ 'nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index b9f2ea47e8f2ac40ae3a8ec17f6e01d0e22401b3..b28d4930a21f5af2b84b435ef3ba53575f31d7bc 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -5,7 +5,7 @@ process TRIM_READS {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'quay.io/nf-core/ubuntu:20.04' }"
+ 'nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(reads)
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 6f6bad458bb8d83962f1d5a1bc922caeb7d3d9f9..453513fbd586e81e0c069f8029339d37f87c75c3 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_medium'
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path multiqc_config
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index 5e392c140a86e51925b1ce751a81868dda5268ef..b2f9610fcf55558abd0d815a1e4c56e81b772d4f 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'quay.io/nf-core/ubuntu:20.04' }"
+ 'nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(bedpe)
diff --git a/nextflow.config b/nextflow.config
index 931b861808632758b83c5a7ff6d411fed415ed79..7d3ee4d21a4d86722dbbe170c9deeca56d7b7328 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -152,7 +152,11 @@ try {
profiles {
- debug { process.beforeScript = 'echo $HOSTNAME' }
+ debug {
+ dumpHashes = true
+ process.beforeScript = 'echo $HOSTNAME'
+ cleanup = false
+ }
conda {
conda.enabled = true
docker.enabled = false
@@ -160,6 +164,7 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
mamba {
conda.enabled = true
@@ -169,14 +174,18 @@ 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'
@@ -184,31 +193,49 @@ 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'
@@ -276,7 +303,7 @@ manifest {
description = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
- version = '2.1.0dev'
+ 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"