Update to 3.2.0 and add json support

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:

.nf-core.yml

@@ -1,4 +1,4 @@
-nf_core_version: 3.1.2
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Louis Le Nezet, Anabella Trigila

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec

CHANGELOG.md

@@ -7,10 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#175](https://github.com/nf-core/phaseimpute/pull/175) - Add support for all input files in `.json` or `.yaml` format.
+
 ### `Changed`
 
 - [#166](https://github.com/nf-core/phaseimpute/pull/166) - Bump version to 1.1.0dev and update `CHANGELOG.md`.
 - [#170](https://github.com/nf-core/phaseimpute/pull/170) - Update TEMPLATE to nf-core tools version 3.1.2.
+- [#175](https://github.com/nf-core/phaseimpute/pull/175) - Update TEMPLATE to nf-core tools version 3.2.0. Move `CHRCHECK` functions to the workflow directory.
 
 ### `Fixed`
 

modules.json

@@ -119,7 +119,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {

nextflow.config

@@ -276,14 +276,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

nextflow_schema.json

@@ -18,7 +18,7 @@
                     "exists": true,
                     "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/phaseimpute/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
@@ -28,7 +28,7 @@
                     "description": "Region of the genome to use (optional: if no file given, the whole genome will be used). The file should be a comma-separated file with 3 columns, and a header row.",
                     "schema": "assets/schema_input_region.json",
                     "format": "file-path",
-                    "pattern": "^\\S+\\.csv$"
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$"
                 },
                 "outdir": {
                     "type": "string",
@@ -94,7 +94,7 @@
                 "genotype": {
                     "type": "string",
                     "description": "Genotype position to use to simulate the data",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "format": "file-path",
                     "mimetype": "text/csv"
                 }
@@ -112,7 +112,7 @@
                     "fa_icon": "far fa-file-code",
                     "format": "file-path",
                     "schema": "assets/schema_input_panel.json",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "mimetype": "text/csv"
                 },
                 "phase": {
@@ -155,7 +155,15 @@
                     "format": "file-path",
                     "mimetype": "text/csv",
                     "schema": "/assets/schema_chunks.json",
-                    "pattern": "^\\S+\\.csv$"
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$"
+                },
+                "posfile": {
+                    "type": "string",
+                    "description": "Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.",
+                    "format": "file-path",
+                    "schema": "assets/schema_posfile.json",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
+                    "mimetype": "text/csv"
                 },
                 "seed": {
                     "type": "integer",
@@ -177,7 +185,7 @@
                     "exists": true,
                     "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "description": "Path to comma-separated file containing information about the samples truth files in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/phaseimpute/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
@@ -441,14 +449,6 @@
             "description": "Arguments to customize STITCH run",
             "default": "",
             "properties": {
-                "posfile": {
-                    "type": "string",
-                    "description": "Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.",
-                    "format": "file-path",
-                    "schema": "assets/schema_posfile.json",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                    "mimetype": "text/csv"
-                },
                 "k_val": {
                     "type": "integer",
                     "default": 2,

ro-crate-metadata.json

@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-01-20T14:35:29+00:00",
+            "datePublished": "2025-01-27T16:15:46+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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)\n\n## Introduction\n\n**nf-core/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/phaseimpute/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#dc3602fa-075a-4dfc-8bee-3a2040fe2b9a"
+                    "@id": "#d6575093-6089-483c-83d2-e48d2500d579"
                 }
             ],
             "name": "nf-core/phaseimpute"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-01-20T14:35:29Z",
+            "dateModified": "2025-01-27T16:15:46Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "genotype", "imputation", "low-pass-sequencing", "phasing"],
             "license": ["MIT"],
@@ -150,11 +150,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#dc3602fa-075a-4dfc-8bee-3a2040fe2b9a",
+            "@id": "#d6575093-6089-483c-83d2-e48d2500d579",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#7ca094cd-78f9-4d32-9c28-5dd3eb4dcfe4"
+                    "@id": "#98cb49f8-adf9-4a8e-9b55-1d65e7e46456"
                 }
             ],
             "mainEntity": {
@@ -163,7 +163,7 @@
             "name": "Test suite for nf-core/phaseimpute"
         },
         {
-            "@id": "#7ca094cd-78f9-4d32-9c28-5dd3eb4dcfe4",
+            "@id": "#98cb49f8-adf9-4a8e-9b55-1d65e7e46456",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/phaseimpute",
             "resource": "repos/nf-core/phaseimpute/actions/workflows/ci.yml",