PR to prepare for dev to master for release 1.0.2

.nf-core.yml

@@ -8,4 +8,4 @@ template:
   name: demo
   org: nf-core
   outdir: .
-  version: 1.0.2dev
+  version: 1.0.2

CHANGELOG.md

@@ -3,12 +3,6 @@
 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).
 
-## dev
-
-### `Changed`
-
-[#34](https://github.com/nf-core/demo/pull/34) Updated the JSON schema to make input validation stricter, thus preventing more errors during the pipeline run.
-
 ## 1.0.2
 
 ### Credits
@@ -17,9 +11,17 @@ Special thanks to the following for their reviews and assistance:
 
 - [Chris Hakkaart](https://github.com/christopher-hakkaart)
 - [Marcel Ribeiro-Dantas](https://github.com/mribeirodantas)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Geraldine Van der Auwera](https://github.com/vdauwera)
+- [Florian Wuennemann](https://github.com/FloWuenne)
 
 ### Changed
 
+[#39][https://github.com/nf-core/demo/pull/39] - Remove -C from bach in nextflow.config
+[#38][https://github.com/nf-core/demo/pull/38] - Template update for nf-core/tools v3.3.1
+[#36][https://github.com/nf-core/demo/pull/36] - Template update for nf-core/tools v3.2.1
+[#34][https://github.com/nf-core/demo/pull/34] - updated nextflow_schema.json
+[#32][https://github.com/nf-core/demo/pull/32] - Minor fixes and template update
 [#29](https://github.com/nf-core/demo/pull/29) - Template update for nf-core/tools v3.2.0
 [#23](https://github.com/nf-core/demo/pull/23) - Update to latest `seqtk` and `fastqc` modules
 [#21](https://github.com/nf-core/demo/pull/21) - Template update for nf-core/tools v3.1.0

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/demo/tree/dev"
+  This report has been generated by the <a href="https://github.com/nf-core/demo/releases/tag/1.0.2"
   target="_blank">nf-core/demo</a> analysis pipeline. For information about how to
-  interpret these results, please see the <a href="https://nf-co.re/demo/dev/docs/output"
+  interpret these results, please see the <a href="https://nf-co.re/demo/1.0.2/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-demo-methods-description":

modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
+                        "git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "e594e9dfaffa7572afc11bafc634984fd4cbd87b",
                         "installed_by": ["modules"]
                     },
                     "seqtk/trim": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     }
                 }

nextflow.config

@@ -250,7 +250,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0.2dev'
+    version         = '1.0.2'
     doi             = '10.5281/zenodo.12192442'
 }
 

ro-crate-metadata.json

@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-06-25T14:34:33+00:00",
+            "creativeWorkStatus": "Stable",
+            "datePublished": "2025-06-26T20:03:01+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n    <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.12192442-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.12192442)\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/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.\n\n![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)\n\n1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))\n3. 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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nSAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz\nSAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).\n\n<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.12192442](https://doi.org/10.5281/zenodo.12192442)\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": "#dc664a18-147f-4bf5-9d5d-5298edf06ed4"
+                    "@id": "#0df73e30-5e9c-44f6-b881-81824440495b"
                 }
             ],
             "name": "nf-core/demo"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-06-25T14:34:33Z",
+            "dateModified": "2025-06-26T20:03:01Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -156,10 +156,10 @@
             },
             "url": [
                 "https://github.com/nf-core/demo",
-                "https://nf-co.re/demo/dev/"
+                "https://nf-co.re/demo/1.0.2/"
             ],
             "version": [
-                "1.0.2dev"
+                "1.0.2"
             ]
         },
         {
@@ -175,11 +175,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#dc664a18-147f-4bf5-9d5d-5298edf06ed4",
+            "@id": "#0df73e30-5e9c-44f6-b881-81824440495b",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#11d98977-d4ef-4731-b43d-8bf6862f2f7c"
+                    "@id": "#783b785f-805a-40a5-a0a1-0ad9c9dcc7a2"
                 }
             ],
             "mainEntity": {
@@ -188,7 +188,7 @@
             "name": "Test suite for nf-core/demo"
         },
         {
-            "@id": "#11d98977-d4ef-4731-b43d-8bf6862f2f7c",
+            "@id": "#783b785f-805a-40a5-a0a1-0ad9c9dcc7a2",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/demo",
             "resource": "repos/nf-core/demo/actions/workflows/nf-test.yml",

tests/.nftignore

@@ -6,6 +6,7 @@ multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+multiqc/multiqc_data/BETA-multiqc.parquet
 fastqc/**/*_fastqc.{html,zip}
 
 pipeline_info/*.{html,json,txt,yml}

tests/default.nf.test.snap

@@ -10,7 +10,7 @@
                     "seqtk": "1.4-r122"
                 },
                 "Workflow": {
-                    "nf-core/demo": "v1.0.2dev"
+                    "nf-core/demo": "v1.0.2"
                 }
             },
             [
@@ -36,6 +36,7 @@
                 "fq/SAMPLE3_SE/SAMPLE3_SE_sample2_R1.fastq.gz",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -68,7 +69,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -82,7 +82,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -96,7 +95,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_demo_software_mqc_versions.yml"
@@ -127,6 +125,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-06-25T15:13:33.021500703"
+        "timestamp": "2025-06-26T20:06:21.191873263"
     }
 }