From eca7e5aaa4cd28436721d38e819c1f5c2f2aa505 Mon Sep 17 00:00:00 2001 From: nservant Date: Sat, 21 Jan 2023 12:56:46 +0100 Subject: [PATCH 01/22] [BUMP] v2.1.0dev --- CHANGELOG.md | 3 +++ nextflow.config | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c111c7f..ede5e30 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,9 @@ 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). +## v2.1.0dev + + ## v2.0.0 - 2023-01-12 ### `Added` diff --git a/nextflow.config b/nextflow.config index 4513d65..9313b6a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -267,7 +267,7 @@ manifest { description = """Analysis of Chromosome Conformation Capture data (Hi-C)""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.0.0' + version = '2.1.0dev' doi = '' } From a18305245d4b9783dac4fbfb68d88fb86cda0833 Mon Sep 17 00:00:00 2001 From: nservant Date: Sat, 21 Jan 2023 12:59:49 +0100 Subject: [PATCH 02/22] [MODIF] update CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ede5e30..4095f4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.1.0dev - ## v2.0.0 - 2023-01-12 ### `Added` From f2163ed20686f8a5b555bbdfd1810140bb844700 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Wed, 29 Mar 2023 23:25:21 +0200 Subject: [PATCH 03/22] Fix incorrect handling of --restriction_site and --ligation_site params Fixes https://github.com/nf-core/hic/issues/150 --- workflows/hic.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/workflows/hic.nf b/workflows/hic.nf index fed1114..2ffa5b4 100644 --- a/workflows/hic.nf +++ b/workflows/hic.nf @@ -28,6 +28,9 @@ if (params.digestion){ ch_restriction_site = Channel.value(restriction_site) ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false ch_ligation_site = Channel.value(ligation_site) +}else if (params.restriction_site && params.ligation_site){ + ch_restriction_site = Channel.value(params.restriction_site) + ch_ligation_site = Channel.value(params.ligation_site) }else if (params.dnase){ ch_restriction_site = Channel.empty() ch_ligation_site = Channel.empty() From 88935526d056248aad6e5c93ecd6d1fa7c7525c5 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Thu, 30 Mar 2023 01:15:14 +0200 Subject: [PATCH 04/22] Trigger CI From fa42adcda98908810526f9a720a5ba53d9969cf9 Mon Sep 17 00:00:00 2001 From: Jasmin Zohren <5310751+jzohren@users.noreply.github.com> Date: Sun, 2 Apr 2023 15:18:17 +0200 Subject: [PATCH 05/22] Update output.md fixed a few spelling mistakes --- docs/output.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/docs/output.md b/docs/output.md index 9f6f703..1086b03 100644 --- a/docs/output.md +++ b/docs/output.md @@ -23,7 +23,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [MultiQC](#multiqc) - aggregate report and quality controls, describing results of the whole pipeline - [Export](#exprot) - additionnal export for compatibility with downstream - analysis tool and visualization + analysis tool and visualisation ## From raw data to valid pairs @@ -36,7 +36,7 @@ For details about the workflow, see #### Reads alignment -Using Hi-C data, each reads mate has to be independantly aligned on the +Using Hi-C data, each reads mate has to be independently aligned on the reference genome. The current workflow implements a two steps mapping strategy. First, the reads are aligned using an end-to-end aligner. @@ -63,7 +63,7 @@ are available ; - `*.mapstat` - mapping statistics per read mate Usually, a high fraction of reads is expected to be aligned on the genome -(80-90%). Among them, we usually observed a few percent (around 10%) of step 2 +(80-90%). Among them, we usually observe a few percent (around 10%) of step 2 aligned reads. Those reads are chimeric fragments for which we detect a ligation junction. An abnormal level of chimeric reads can reflect a ligation issue during the library preparation. @@ -142,9 +142,9 @@ removed (see `--keep_dups` to disable duplicates filtering). Additional quality controls such as fragment size distribution can be extracted from the list of valid interaction products. -We usually expect to see a distribution centered around 300 pb which correspond +We usually expect to see a distribution centered around 300 bp which corresponds to the paired-end insert size commonly used. -The fraction of dplicates is also presented. A high level of duplication +The fraction of duplicates is also presented. A high level of duplication indicates a poor molecular complexity and a potential PCR bias. Finally, an important metric is to look at the fraction of intra and inter-chromosomal interactions, as well as long range (>20kb) versus short @@ -176,15 +176,15 @@ All results are available in `results/hicpro/stats`. #### Contact maps -Intra et inter-chromosomal contact maps are build for all specified resolutions. -The genome is splitted into bins of equal size. Each valid interaction is +Intra and inter-chromosomal contact maps are built for all specified resolutions. +The genome is split into bins of equal size. Each valid interaction is associated with the genomic bins to generate the raw maps. In addition, Hi-C data can contain several sources of biases which has to be corrected. The HiC-Pro workflow uses the [ìced](https://github.com/hiclib/iced) and [Varoquaux and Servant, 2018](http://joss.theoj.org/papers/10.21105/joss.01286) python package which proposes a fast implementation of the original ICE -normalization algorithm (Imakaev et al. 2012), making the assumption of equal +normalisation algorithm (Imakaev et al. 2012), making the assumption of equal visibility of each fragment. Importantly, the HiC-Pro maps are generated only if the `--hicpro_maps` option @@ -221,16 +221,16 @@ downstream analysis. ## Hi-C contact maps Contact maps are usually stored as simple txt (`HiC-Pro`), .hic (`Juicer/Juicebox`) and .(m)cool (`cooler/Higlass`) formats. -The .cool and .hic format are compressed and indexed and usually much more efficient that the txt format. -In the current workflow, we propose to use the `cooler` format as a standard to build the raw and normalized maps -after valid pairs detection as it is used by several downstream analysis and visualization tools. +The .cool and .hic format are compressed and indexed and usually much more efficient than the txt format. +In the current workflow, we propose to use the `cooler` format as a standard to build the raw and normalised maps +after valid pairs detection as it is used by several downstream analysis and visualisation tools. Raw contact maps are therefore in **`results/contact_maps/raw`** which contains the different maps in `txt` and `cool` formats, at various resolutions. -Normalized contact maps are stored in **`results/contact_maps/norm`** which contains the different maps in `txt`, `cool`, and `mcool` format. +Normalised contact maps are stored in **`results/contact_maps/norm`** which contains the different maps in `txt`, `cool`, and `mcool` format. The bin coordinates used for all resolutions are available in **`results/contact_maps/bins`**. Note that `txt` contact maps generated with `cooler` are identical to those generated by `HiC-Pro`. -However, differences can be observed on the normalized contact maps as the balancing algorithm is not exactly the same. +However, differences can be observed on the normalised contact maps as the balancing algorithm is not exactly the same. ## Downstream analysis @@ -246,23 +246,23 @@ The results generated with the `HiCExplorer hicPlotDistVsCounts` tool (plot and ### Compartments calling Compartments calling is one of the most common analysis which aims at detecting A (open, active) / B (close, inactive) compartments. -In the first studies on the subject, the compartments were called at high/medium resolution (1000000 to 250000) which is enough to call A/B comparments. +In the first studies on the subject, the compartments were called at high/medium resolution (1000000 to 250000) which is enough to call A/B compartments. Analysis at higher resolution has shown that these two main types of compartments can be further divided into compartments subtypes. -Although different methods have been proposed for compartment calling, the standard remains the eigen vector decomposition from the normalized correlation maps. +Although different methods have been proposed for compartment calling, the standard remains the eigen vector decomposition from the normalised correlation maps. Here, we use the implementation available in the [`cooltools`](https://cooltools.readthedocs.io/en/lates) package. -Results are available in **`results/compartments/`** folder and includes : +Results are available in **`results/compartments/`** folder and include : - `*cis.vecs.tsv`: eigenvectors decomposition along the genome - `*cis.lam.txt`: eigenvalues associated with the eigenvectors ### TADs calling -TADs has been described as functional units of the genome. -While contacts between genes and regulatority elements can occur within a single TADs, contacts between TADs are much less frequent, mainly due to the presence of insulation protein (such as CTCF) at their boundaries. Looking at Hi-C maps, TADs look like triangles around the diagonal. According to the contact map resolutions, TADs appear as hierarchical structures with a median size around 1Mb (in mammals), as well as smaller structures usually called sub-TADs of smaller size. +TADs have been described as functional units of the genome. +While contacts between genes and regulatority elements can occur within a single TAD, contacts between TADs are much less frequent, mainly due to the presence of an insulation protein (such as CTCF) at their boundaries. Looking at Hi-C maps, TADs look like triangles around the diagonal. According to the contact map resolutions, TADs appear as hierarchical structures with a median size around 1Mb (in mammals), as well as smaller structures usually called sub-TADs of smaller size. -TADs calling remains a challenging task, and even if many methods have been proposed in the last decade, little overlap have been found between their results. +TADs calling remains a challenging task, and even if many methods have been proposed in the last decade, little overlap has been found between their results. Currently, the pipeline proposes two approaches : @@ -283,7 +283,7 @@ Usually, TADs results are presented as simple BED files, or bigWig files, with t -[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. +[MultiQC](http://multiqc.info) is a visualisation 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 . From 7d1306df29d024c69f033b803e98fb413edd06e8 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:22:36 +0000 Subject: [PATCH 06/22] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .pre-commit-config.yaml | 5 + CHANGELOG.md | 2 +- README.md | 74 ++++++---- bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/igenomes.config | 8 ++ conf/test_full.config | 2 + docs/usage.md | 130 +++++------------- lib/NfcoreSchema.groovy | 4 +- lib/WorkflowHic.groovy | 12 +- lib/WorkflowMain.groovy | 13 +- main.nf | 1 - modules.json | 4 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 2 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 3 +- nextflow.config | 31 ++++- tower.yml | 5 + 28 files changed, 195 insertions(+), 159 deletions(-) create mode 100644 .github/workflows/clean-up.yml create mode 100644 .pre-commit-config.yaml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e..b6b3190 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 e405327..eb120e6 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 c67458d..e2cdecc 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 `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index c528fff..014f094 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 3f9b365..e731163 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 b92e3d2..edf46df 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" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 0000000..694e90e --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622..888cb4b 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 0000000..0c31cdb --- /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 1b0b90b..3a475fb 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 b2c63a1..354b980 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,71 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/hic) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hic)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hic)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction - +**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! - - - -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 + + 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. + + - 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 ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + -4. Start running your own analysis! +```bash +nextflow run nf-core/hic \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - +> **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 --genome GRCh37 -profile - ``` +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 11b1557..4a758fe 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 66977ff..74a33d1 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 7a1b3ac..3f11437 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 7c09bad..4c22dc2 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 e0dab28..506b575 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 `. + +> ⚠️ Do not use `-c ` 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. \ - - -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. -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 33cd4f6..9b34804 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 71742bd..e51a467 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 dd0c03d..978ce77 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 d8cba4a..7dd9be5 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 4297c82..072b219 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 1624dfa..096c80b 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 3df2176..800a609 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 60b546a..c32657d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66be..4b60474 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ 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 ebc29b2..f93b5ee 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 dacdcf0..b1f98b3 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 0000000..787aedf --- /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" From 16ed196a939969e9a3d81e6c997ebe0af36571c8 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 17:41:39 +0100 Subject: [PATCH 07/22] Update all NF-Core modules to latest version which includes no quay.io prefix --- modules.json | 20 +++++++++---------- modules/nf-core/bowtie2/align/main.nf | 2 +- modules/nf-core/bowtie2/build/main.nf | 2 +- modules/nf-core/cooler/balance/main.nf | 2 +- modules/nf-core/cooler/cload/main.nf | 2 +- modules/nf-core/cooler/dump/main.nf | 2 +- modules/nf-core/cooler/makebins/main.nf | 2 +- modules/nf-core/cooler/zoomify/main.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +++--- .../custom/dumpsoftwareversions/meta.yml | 2 ++ .../templates/dumpsoftwareversions.py | 4 ++-- modules/nf-core/custom/getchromsizes/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 2 +- 13 files changed, 26 insertions(+), 24 deletions(-) diff --git a/modules.json b/modules.json index 45540ca..6d7a030 100644 --- a/modules.json +++ b/modules.json @@ -7,52 +7,52 @@ "nf-core": { "bowtie2/align": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cooler/balance": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cooler/cload": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cooler/dump": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cooler/makebins": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cooler/zoomify": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 3d85186..311a150 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_ALIGN { conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' : - 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" + 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" input: tuple val(meta) , path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 551893a..566a4ac 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_BUILD { conda "bioconda::bowtie2=2.4.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : - 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" + 'biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/cooler/balance/main.nf b/modules/nf-core/cooler/balance/main.nf index 4173a3c..6e131d5 100644 --- a/modules/nf-core/cooler/balance/main.nf +++ b/modules/nf-core/cooler/balance/main.nf @@ -5,7 +5,7 @@ process COOLER_BALANCE { conda "bioconda::cooler=0.8.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0': - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: tuple val(meta), path(cool), val(resolution) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 80d61f0..80109d4 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -5,7 +5,7 @@ process COOLER_CLOAD { conda "bioconda::cooler=0.8.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: tuple val(meta), path(pairs), path(index), val(cool_bin) diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index b46c78c..fed7502 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -5,7 +5,7 @@ process COOLER_DUMP { conda "bioconda::cooler=0.8.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: tuple val(meta), path(cool), val(resolution) diff --git a/modules/nf-core/cooler/makebins/main.nf b/modules/nf-core/cooler/makebins/main.nf index 7f08261..25d6a40 100644 --- a/modules/nf-core/cooler/makebins/main.nf +++ b/modules/nf-core/cooler/makebins/main.nf @@ -5,7 +5,7 @@ process COOLER_MAKEBINS { conda "bioconda::cooler=0.8.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0': - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: tuple val(meta), path(chromsizes), val(cool_bin) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index f1cd8df..95e7daf 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -5,7 +5,7 @@ process COOLER_ZOOMIFY { conda "bioconda::cooler=0.8.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: tuple val(meta), path(cool) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df2176..ebc8727 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ 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' : + '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 60b546a..c32657d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index b83b32c..da03340 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -3,10 +3,10 @@ """Provide functions to merge multiple versions.yml files.""" -import platform -from textwrap import dedent import yaml +import platform +from textwrap import dedent def _make_versions_html(versions): diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 580f87f..060a2e8 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9ae5838..07d5e43 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + 'biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) From 2f11c1dfa2b445f5c9c8d0b7df3cd587fd217a08 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 17:43:45 +0100 Subject: [PATCH 08/22] Add default registry to quay.io --- nextflow.config | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index 4513d65..9efeef9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -54,13 +54,13 @@ params { ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC' } } - + min_restriction_fragment_size = 0 max_restriction_fragment_size = 0 min_insert_size = 0 max_insert_size = 0 save_pairs_intermediates = false - + // Dnase Hi-C dnase = false min_cis_dist = 0 @@ -111,7 +111,7 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,digest' - + // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" @@ -242,6 +242,12 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set default registry for Docker and Podman independent of -profile +// Will not be used unless Docker / Podman are enabled +// Set to your registry if you have a mirror of containers +docker.registry = 'quay.io' +podman.registry = 'quay.io' + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true From 50ec0d49fd73682c3d7850fe2cafe64fbec0249c Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 17:47:31 +0100 Subject: [PATCH 09/22] Update local modules --- modules/local/cooltools/eigscis.nf | 2 +- modules/local/cooltools/insulation.nf | 2 +- modules/local/hicexplorer/hicFindTADs.nf | 2 +- modules/local/hicexplorer/hicPlotDistVsCounts.nf | 2 +- modules/local/hicpro/bowtie2_merge.nf | 2 +- modules/local/hicpro/build_contact_maps.nf | 8 ++++---- modules/local/hicpro/combine_mates.nf | 2 +- modules/local/hicpro/dnase_mapping_stats.nf | 2 +- modules/local/hicpro/get_restriction_fragments.nf | 2 +- modules/local/hicpro/get_valid_interaction.nf | 2 +- modules/local/hicpro/get_valid_interaction_dnase.nf | 2 +- modules/local/hicpro/hicpro2pairs.nf | 2 +- modules/local/hicpro/merge_stats.nf | 2 +- modules/local/hicpro/merge_valid_interaction.nf | 2 +- modules/local/hicpro/run_ice.nf | 2 +- modules/local/hicpro/trim_reads.nf | 2 +- modules/local/multiqc.nf | 2 +- modules/local/samplesheet_check.nf | 2 +- modules/local/split_cooler_dump.nf | 2 +- 19 files changed, 22 insertions(+), 22 deletions(-) diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf index feaa300..873bd24 100644 --- a/modules/local/cooltools/eigscis.nf +++ b/modules/local/cooltools/eigscis.nf @@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS { conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' : - 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }" + 'biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }" input: tuple val(meta), path(cool), val(resolution) diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf index 8a9127e..af53529 100644 --- a/modules/local/cooltools/insulation.nf +++ b/modules/local/cooltools/insulation.nf @@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION { conda "bioconda::cooltools=0.5.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' : - 'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }" + 'biocontainers/cooltools:0.5.1--py37h37892f8_0' }" input: tuple val(meta), path(cool) diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf index b6cae33..d86dc83 100644 --- a/modules/local/hicexplorer/hicFindTADs.nf +++ b/modules/local/hicexplorer/hicFindTADs.nf @@ -8,7 +8,7 @@ process HIC_FIND_TADS { conda "bioconda::hicexplorer=3.7.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' : - 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" + 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" input: tuple val(meta), path(cool) diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf index 3e37d3f..1143a05 100644 --- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf +++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf @@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS { conda "bioconda::hicexplorer=3.7.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' : - 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" + 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" input: tuple val(meta), path(cool) diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf index 7a4e96b..64aa6e6 100644 --- a/modules/local/hicpro/bowtie2_merge.nf +++ b/modules/local/hicpro/bowtie2_merge.nf @@ -5,7 +5,7 @@ process MERGE_BOWTIE2{ conda "bioconda::samtools=1.15.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + 'biocontainers/samtools:1.15.1--h1170115_0' }" input: tuple val(meta), path(bam1), path(bam2) diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf index fd633a9..8ff4540 100644 --- a/modules/local/hicpro/build_contact_maps.nf +++ b/modules/local/hicpro/build_contact_maps.nf @@ -5,15 +5,15 @@ process BUILD_CONTACT_MAPS{ conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'quay.io/nfcore/ubuntu:20.04' }" input: - tuple val(meta), path(vpairs), val(resolution) - tuple val(meta2), path(chrsize) + tuple val(meta), path(vpairs), val(resolution) + tuple val(meta2), path(chrsize) output: tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps - + script: def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf index da95be8..b0d828e 100644 --- a/modules/local/hicpro/combine_mates.nf +++ b/modules/local/hicpro/combine_mates.nf @@ -5,7 +5,7 @@ process COMBINE_MATES { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf index 64cb079..8e85113 100644 --- a/modules/local/hicpro/dnase_mapping_stats.nf +++ b/modules/local/hicpro/dnase_mapping_stats.nf @@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE { conda "bioconda::samtools=1.15.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + 'biocontainers/samtools:1.15.1--h1170115_0' }" input: diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf index affc2d9..56cd74a 100644 --- a/modules/local/hicpro/get_restriction_fragments.nf +++ b/modules/local/hicpro/get_restriction_fragments.nf @@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS { conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), path(fasta) diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf index cc14837..bebd421 100644 --- a/modules/local/hicpro/get_valid_interaction.nf +++ b/modules/local/hicpro/get_valid_interaction.nf @@ -5,7 +5,7 @@ process GET_VALID_INTERACTION { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf index 142d0cb..d62318f 100644 --- a/modules/local/hicpro/get_valid_interaction_dnase.nf +++ b/modules/local/hicpro/get_valid_interaction_dnase.nf @@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf index 2ba2a90..eb9b86b 100644 --- a/modules/local/hicpro/hicpro2pairs.nf +++ b/modules/local/hicpro/hicpro2pairs.nf @@ -5,7 +5,7 @@ process HICPRO2PAIRS { conda "bioconda::pairix=0.3.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : - 'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }" + 'biocontainers/pairix:0.3.7--py36h30a8e3e_3' }" input: tuple val(meta), path(vpairs) diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf index b25dc8a..d9c2aec 100644 --- a/modules/local/hicpro/merge_stats.nf +++ b/modules/local/hicpro/merge_stats.nf @@ -5,7 +5,7 @@ process MERGE_STATS { conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), path(fstat) diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf index 29e568a..6a5c830 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nfcore/ubuntu:20.04' }" input: tuple val(meta), path(vpairs) diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf index 0a435ed..74c96dc 100644 --- a/modules/local/hicpro/run_ice.nf +++ b/modules/local/hicpro/run_ice.nf @@ -5,7 +5,7 @@ process ICE_NORMALIZATION{ conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" input: tuple val(meta), val(res), path(rmaps), path(bed) diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf index 5a96df4..f6d2e90 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nfcore/ubuntu:20.04' }" input: tuple val(meta), path(reads) diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf index 595dc94..6f6bad4 100644 --- a/modules/local/multiqc.nf +++ b/modules/local/multiqc.nf @@ -4,7 +4,7 @@ process MULTIQC { conda "bioconda::multiqc=1.13" container "${ 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' }" + 'biocontainers/multiqc:1.13--pyhdfd78af_0' }" input: path multiqc_config diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 1624dfa..096c80b 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf index 8b9e45b..c9dde00 100644 --- a/modules/local/split_cooler_dump.nf +++ b/modules/local/split_cooler_dump.nf @@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP { conda "conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nfcore/ubuntu:20.04' }" input: tuple val(meta), path(bedpe) From 01d51d57df6442abb061f17621da2a4718b2f1a8 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 17:48:50 +0100 Subject: [PATCH 10/22] quay.io --- modules/local/hicpro/build_contact_maps.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf index 8ff4540..c4e4616 100644 --- a/modules/local/hicpro/build_contact_maps.nf +++ b/modules/local/hicpro/build_contact_maps.nf @@ -5,7 +5,7 @@ process BUILD_CONTACT_MAPS{ conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'quay.io/nfcore/ubuntu:20.04' }" + 'nfcore/ubuntu:20.04' }" input: tuple val(meta), path(vpairs), val(resolution) From 5f8dff525c2518a4ab31aa850731e3d68149bea1 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 17:57:46 +0100 Subject: [PATCH 11/22] ubuntu:20.04 to nf-core version --- modules/local/hicpro/build_contact_maps.nf | 2 +- modules/local/hicpro/merge_valid_interaction.nf | 2 +- modules/local/hicpro/trim_reads.nf | 2 +- modules/local/split_cooler_dump.nf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf index c4e4616..34b27aa 100644 --- a/modules/local/hicpro/build_contact_maps.nf +++ b/modules/local/hicpro/build_contact_maps.nf @@ -5,7 +5,7 @@ process BUILD_CONTACT_MAPS{ conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nfcore/ubuntu:20.04' }" + 'quay.io/nf-core/ubuntu:20.04' }" input: tuple val(meta), path(vpairs), val(resolution) diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf index 6a5c830..25c437e 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nfcore/ubuntu:20.04' }" + 'quay.io/nf-core/ubuntu:20.04' }" input: tuple val(meta), path(vpairs) diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf index f6d2e90..b9f2ea4 100644 --- a/modules/local/hicpro/trim_reads.nf +++ b/modules/local/hicpro/trim_reads.nf @@ -5,7 +5,7 @@ process TRIM_READS { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nfcore/ubuntu:20.04' }" + 'quay.io/nf-core/ubuntu:20.04' }" input: tuple val(meta), path(reads) diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf index c9dde00..5e392c1 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' : - 'nfcore/ubuntu:20.04' }" + 'quay.io/nf-core/ubuntu:20.04' }" input: tuple val(meta), path(bedpe) From 91784a334bd5d96258e930ed6f750b0ad39fc988 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 18:04:00 +0100 Subject: [PATCH 12/22] black --- bin/mapped_2hic_dnase.py | 1 - bin/mapped_2hic_fragments.py | 1 - bin/mergeSAM.py | 1 - 3 files changed, 3 deletions(-) diff --git a/bin/mapped_2hic_dnase.py b/bin/mapped_2hic_dnase.py index ff59366..c417907 100755 --- a/bin/mapped_2hic_dnase.py +++ b/bin/mapped_2hic_dnase.py @@ -362,7 +362,6 @@ def get_read_tag(read, tag): if cur_handler is not None: if not r1.is_unmapped and not r2.is_unmapped: - ##reorient reads to ease duplicates removal or1, or2 = get_ordered_reads(r1, r2) or1_chrom = samfile.get_reference_name(or1.reference_id) diff --git a/bin/mapped_2hic_fragments.py b/bin/mapped_2hic_fragments.py index cc0e40b..a129871 100755 --- a/bin/mapped_2hic_fragments.py +++ b/bin/mapped_2hic_fragments.py @@ -619,7 +619,6 @@ def get_read_tag(read, tag): r2_chrom = None if r1_resfrag is not None or r2_resfrag is not None: - interactionType = get_interaction_type(r1, r1_chrom, r1_resfrag, r2, r2_chrom, r2_resfrag, verbose) dist = get_PE_fragment_size(r1, r2, r1_resfrag, r2_resfrag, interactionType) cdist = get_cis_dist(r1, r2) diff --git a/bin/mergeSAM.py b/bin/mergeSAM.py index 82ab8c3..d670ec2 100755 --- a/bin/mergeSAM.py +++ b/bin/mergeSAM.py @@ -71,7 +71,6 @@ def get_read_name(read): def sam_flag(read1, read2, hr1, hr2): - f1 = read1.flag f2 = read2.flag From 36974f0e755613cdd0beda00eb5937bb9c75f629 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Tue, 23 May 2023 11:38:17 +0100 Subject: [PATCH 13/22] Add public_aws_ecr profile for using public ECR images --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- CHANGELOG.md | 8 +++++ conf/public_aws_ecr.config | 54 +++++++++++++++++++++++++++++++ modules/local/hicpro/run_ice.nf | 4 +-- nextflow.config | 9 ++++-- 6 files changed, 72 insertions(+), 7 deletions(-) create mode 100644 conf/public_aws_ecr.config diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ad7e2dd..2b99a42 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -24,7 +24,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full,public_aws_ecr - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 3f9b365..177543c 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -22,7 +22,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test,public_aws_ecr - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/CHANGELOG.md b/CHANGELOG.md index c111c7f..db96f41 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ 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). +## v2.0.1dev + +### `Added` + +- Added public_aws_ecr profile for using containers stored on ECR. + +### `Fixed` + ## v2.0.0 - 2023-01-12 ### `Added` diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config new file mode 100644 index 0000000..a126435 --- /dev/null +++ b/conf/public_aws_ecr.config @@ -0,0 +1,54 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + AWS ECR Config +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config to set public AWS ECR images wherever possible + This improves speed when running on AWS infrastructure. + Use this as an example template when using your own private registry. +---------------------------------------------------------------------------------------- +*/ + +docker.registry = 'public.ecr.aws' +podman.registry = 'public.ecr.aws' + +process { + withName: '.*:BOWTIE2_ALIGN' { + container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' + } + withName: '.*:BUILD_CONTACT_MAPS' { + container = 'quay.io/nf-core/ubuntu:20.04' + } + withName: '.*:COMBINE_MATES' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:COOLTOOLS_EIGSCIS' { + container = 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' + } + withName: '.*:GET_RESTRICTION_FRAGMENTS' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:GET_VALID_INTERACTION' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:GET_VALID_INTERACTION_DNASE' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:ICE_NORMALIZATION' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:MERGE_STATS' { + container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' + } + withName: '.*:MERGE_VALID_INTERACTION' { + container = 'quay.io/nf-core/ubuntu:20.04' + } + withName: '.*:SAMPLESHEET_CHECK' { + container = 'quay.io/biocontainers/python:3.8.3' + } + withName: '.*:SPLIT_COOLER_DUMP' { + container = 'quay.io/nf-core/ubuntu:20.04' + } + withName: '.*:TRIM_READS' { + container = 'quay.io/nf-core/ubuntu:20.04' + } +} diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf index 0a435ed..c6ec635 100644 --- a/modules/local/hicpro/run_ice.nf +++ b/modules/local/hicpro/run_ice.nf @@ -1,11 +1,11 @@ -process ICE_NORMALIZATION{ +process ICE_NORMALIZATION { tag "$meta.id" label 'process_high_memory' conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), val(res), path(rmaps), path(bed) diff --git a/nextflow.config b/nextflow.config index 4513d65..d8a5fa8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -54,13 +54,13 @@ params { ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC' } } - + min_restriction_fragment_size = 0 max_restriction_fragment_size = 0 min_insert_size = 0 max_insert_size = 0 save_pairs_intermediates = false - + // Dnase Hi-C dnase = false min_cis_dist = 0 @@ -111,7 +111,7 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,digest' - + // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" @@ -215,6 +215,9 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } + public_aws_ecr { + includeConfig 'conf/public_aws_ecr.config' + } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } From 88dc793d8d6dec723c2c5393becaf0789028e1b5 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Tue, 23 May 2023 16:55:48 +0100 Subject: [PATCH 14/22] Add BOWTIE2_ALIGN_TRIMMED to use mulled container --- conf/public_aws_ecr.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index a126435..4979017 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -15,6 +15,9 @@ process { withName: '.*:BOWTIE2_ALIGN' { container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' } + withName: '.*:BOWTIE2_ALIGN_TRIMMED' { + container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' + } withName: '.*:BUILD_CONTACT_MAPS' { container = 'quay.io/nf-core/ubuntu:20.04' } From 67857287ec103eac4f33b4610eece520bbc487a6 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 24 May 2023 11:30:55 +0100 Subject: [PATCH 15/22] Update setup-nextflow gha --- .github/workflows/ci.yml | 2 +- .github/workflows/linting.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5531e30..83b111b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@v3 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v1.3.0 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622..3dc2346 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -74,7 +74,7 @@ jobs: uses: actions/checkout@v3 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v1.3.0 - uses: actions/setup-python@v4 with: From fe6b4e753bc0873419d76b06478b5dcd4add1e03 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 24 May 2023 12:19:45 +0100 Subject: [PATCH 16/22] Revert linting.yml --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3dc2346..858d622 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -74,7 +74,7 @@ jobs: uses: actions/checkout@v3 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1.3.0 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@v4 with: From 40c833749059e7c5ce1859cf003ffd453b89fe03 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 31 May 2023 15:31:36 +0200 Subject: [PATCH 17/22] prettier --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index be26c07..df0a419 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,6 @@ On release, automated continuous integration tests run the pipeline on a full-si > 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. - First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: From c24f8f8380083baf2384fcf4104fd055ad6dc772 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Jun 2023 13:55:37 +0200 Subject: [PATCH 18/22] bump version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 931b861..f1a2b02 100644 --- a/nextflow.config +++ b/nextflow.config @@ -276,7 +276,7 @@ manifest { description = """Analysis of Chromosome Conformation Capture data (Hi-C)""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.1.0dev' + version = '2.1.0' doi = '' } From 67c5fda350779cd92726316388fdfb2fdddbb7fc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Jun 2023 13:59:57 +0200 Subject: [PATCH 19/22] update version in CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ea99e67..8a9b967 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). -## v2.1.0dev +## v2.1.0 - 2023-06-01 ### `Added` From c55a7fc6c676cf358c63fe1cf22eb2db9a929a51 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 1 Jun 2023 14:02:53 +0200 Subject: [PATCH 20/22] Apply suggestions from code review --- conf/test_full.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 0a3a68f..f7b39d4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' From 856f9492b76be8ed3de3e3ed0c1b4eb2e39fc3e5 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 1 Jun 2023 14:20:17 +0200 Subject: [PATCH 21/22] Update conf/public_aws_ecr.config --- conf/public_aws_ecr.config | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index 4979017..abff277 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -12,46 +12,46 @@ docker.registry = 'public.ecr.aws' podman.registry = 'public.ecr.aws' process { - withName: '.*:BOWTIE2_ALIGN' { + withName: 'BOWTIE2_ALIGN' { container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' } - withName: '.*:BOWTIE2_ALIGN_TRIMMED' { + withName: 'BOWTIE2_ALIGN_TRIMMED' { container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' } - withName: '.*:BUILD_CONTACT_MAPS' { + withName: 'BUILD_CONTACT_MAPS' { container = 'quay.io/nf-core/ubuntu:20.04' } - withName: '.*:COMBINE_MATES' { + withName: 'COMBINE_MATES' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:COOLTOOLS_EIGSCIS' { + withName: 'COOLTOOLS_EIGSCIS' { container = 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' } - withName: '.*:GET_RESTRICTION_FRAGMENTS' { + withName: 'GET_RESTRICTION_FRAGMENTS' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:GET_VALID_INTERACTION' { + withName: 'GET_VALID_INTERACTION' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:GET_VALID_INTERACTION_DNASE' { + withName: 'GET_VALID_INTERACTION_DNASE' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:ICE_NORMALIZATION' { + withName: 'ICE_NORMALIZATION' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:MERGE_STATS' { + withName: 'MERGE_STATS' { container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' } - withName: '.*:MERGE_VALID_INTERACTION' { + withName: 'MERGE_VALID_INTERACTION' { container = 'quay.io/nf-core/ubuntu:20.04' } - withName: '.*:SAMPLESHEET_CHECK' { + withName: 'SAMPLESHEET_CHECK' { container = 'quay.io/biocontainers/python:3.8.3' } - withName: '.*:SPLIT_COOLER_DUMP' { + withName: 'SPLIT_COOLER_DUMP' { container = 'quay.io/nf-core/ubuntu:20.04' } - withName: '.*:TRIM_READS' { + withName: 'TRIM_READS' { container = 'quay.io/nf-core/ubuntu:20.04' } } From 57b87d86d985774b0c525f20162a568e601bca07 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 1 Jun 2023 14:36:50 +0200 Subject: [PATCH 22/22] Apply suggestions from code review Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- modules/local/hicpro/combine_mates.nf | 2 +- modules/local/hicpro/get_restriction_fragments.nf | 2 +- modules/local/hicpro/get_valid_interaction.nf | 2 +- modules/local/hicpro/get_valid_interaction_dnase.nf | 2 +- modules/local/hicpro/merge_stats.nf | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf index b0d828e..1f31e66 100644 --- a/modules/local/hicpro/combine_mates.nf +++ b/modules/local/hicpro/combine_mates.nf @@ -5,7 +5,7 @@ process COMBINE_MATES { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf index 56cd74a..d810c4c 100644 --- a/modules/local/hicpro/get_restriction_fragments.nf +++ b/modules/local/hicpro/get_restriction_fragments.nf @@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS { conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), path(fasta) diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf index bebd421..a093977 100644 --- a/modules/local/hicpro/get_valid_interaction.nf +++ b/modules/local/hicpro/get_valid_interaction.nf @@ -5,7 +5,7 @@ process GET_VALID_INTERACTION { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf index d62318f..6bb841e 100644 --- a/modules/local/hicpro/get_valid_interaction_dnase.nf +++ b/modules/local/hicpro/get_valid_interaction_dnase.nf @@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE { conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), path(bam) diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf index d9c2aec..eb9a9e0 100644 --- a/modules/local/hicpro/merge_stats.nf +++ b/modules/local/hicpro/merge_stats.nf @@ -5,7 +5,7 @@ process MERGE_STATS { conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : - 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" + 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }" input: tuple val(meta), path(fstat)