Patch release 1.0.3

.nf-core.yml

@@ -32,7 +32,7 @@ template:
   name: sampletracking
   description: CMGG Sampletracking workflow
   author: Matthias De Smet
-  version: 1.0.2
+  version: 1.0.3
   force: true
   outdir: .
   is_nfcore: false

CHANGELOG.md

@@ -3,6 +3,10 @@
 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).
 
+## v1.0.3
+
+- Fixed an issue where pool grouping for multiqc wasn't properly performed on pipeline resume
+
 ## v1.0.2
 
 - Fixed an issue where multiqc didn't run for each pool

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/sampletracking/releases/tag/1.0.2" target="_blank">nf-cmgg/sampletracking</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/sampletracking/releases/tag/1.0.3" target="_blank">nf-cmgg/sampletracking</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-sampletracking-methods-description":
     order: -1000

conf/test.config

@@ -37,6 +37,7 @@ process {
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
+    custom_config_base         = null
 
     input = "${projectDir}/assets/samplesheet.csv"
     bwa_index = "s3://test-data/genomics/homo_sapiens/genome/bwa/"

nextflow.config

@@ -227,7 +227,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=26.04.0'
-    version         = '1.0.2'
+    version         = '1.0.3'
     doi             = ''
 }
 

ro-crate-metadata.json

@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-05-27T11:44:13+00:00",
+            "datePublished": "2026-07-23T15:20:45+00:00",
             "description": "# ![nf-cmgg/sampletracking](docs/images/nf-cmgg-sampletracking_logo_light.svg#gh-light-mode-only) ![nf-cmgg/sampletracking](docs/images/nf-cmgg-sampletracking_logo_dark.svg#gh-dark-mode-only)\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-cmgg/sampletracking)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/sampletracking/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/sampletracking/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/sampletracking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/sampletracking/actions/workflows/linting.yml)[![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/version-%E2%89%A526.04.0-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-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\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-cmgg/sampletracking)\n\n## Introduction\n\n**nf-cmgg/sampletracking** is a bioinformatics pipeline that performs sampletracking on sequencing samples. The pipeline does this by crosschecking SNP fingerprints and by checking if the expected sex matches the real sex of the sample.\n\n![metro_map](docs/images/metro_map.png)\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,pool,sex,sample_bam,sample_bam_index,snp_bam,snp_bam_index\nSAMPLE1,POOL1,F,SAMPLE1.bam,SAMPLE1.bam.bai,SAMPLE1_snp.cram,SAMPLE2_snp.cram.crai\n```\n\nEach row represents a sample annotated with the pool it was sequenced in and the expected sex of this sample. It also needs a BAM/CRAM file with the sample data and (optionally) a FASTQ/BAM/CRAM file with SNP tracking data for the sample. Crosschecking fingerprints will be skipped when no SNP tracking data is provided.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-cmgg/sampletracking \\\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**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\n## Credits\n\nnf-cmgg/sampletracking was originally written by [@matthdsm](https://github.com/matthdsm).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@nvnieuwk](https://github.com/nvnieuwk)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n\n## Citations\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\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": "#3fade23d-b7f2-4138-bbee-fa7c35bcbcb3"
+                    "@id": "#1afaeae5-d623-4182-864b-131038a46785"
                 }
             ],
             "name": "nf-cmgg/sampletracking"
@@ -112,7 +112,7 @@
             },
             "conformsTo": [
                 {
-                    "@id": "https://w3id.org/ro/crate/1.1"
+                    "@id": "https://w3id.org/ro/crate/1.2"
                 },
                 {
                     "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-05-27T13:44:13Z",
+            "dateModified": "2026-07-23T17:20:45Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "image": {
                 "@id": "docs/images/metro_map.png"
@@ -163,10 +163,10 @@
             },
             "url": [
                 "https://github.com/nf-cmgg/sampletracking",
-                "https://nf-co.re/nf-cmgg/sampletracking/1.0.2/"
+                "https://nf-co.re/nf-cmgg/sampletracking/1.0.3/"
             ],
             "version": [
-                "1.0.2"
+                "1.0.3"
             ]
         },
         {
@@ -190,11 +190,11 @@
             "name": "Workflow diagram"
         },
         {
-            "@id": "#3fade23d-b7f2-4138-bbee-fa7c35bcbcb3",
+            "@id": "#1afaeae5-d623-4182-864b-131038a46785",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#5249f773-adaa-4bdf-a11c-7cdffb4db2e7"
+                    "@id": "#3c6ba561-6507-48ed-b107-371fc7904400"
                 }
             ],
             "mainEntity": {
@@ -203,7 +203,7 @@
             "name": "Test suite for nf-cmgg/sampletracking"
         },
         {
-            "@id": "#5249f773-adaa-4bdf-a11c-7cdffb4db2e7",
+            "@id": "#3c6ba561-6507-48ed-b107-371fc7904400",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-cmgg/sampletracking",
             "resource": "repos/nf-cmgg/sampletracking/actions/workflows/nf-test.yml",

workflows/sampletracking.nf

@@ -94,18 +94,14 @@ workflow SAMPLETRACKING {
 
     def ch_crosscheck_metrics_out = channel.empty()
     ch_samplesheet_fixed
-        .filter { meta, _sample_bam, _sample_bam_index, snp_fastq, snp_bam, _snp_bam_index ->
-            if(!snp_bam && !snp_fastq) {
-                log.warn("No SNP BAM/CRAM/FASTQ files were detected for '${meta.id}'. Skipping the crosscheck fingerprints step for this sample.")
-                return false
-            }
-            return true
-        }
         .branch { meta, sample_bam, sample_bam_index, snp_fastq, snp_bam, snp_bam_index ->
             aligned: snp_bam
                 return [meta, sample_bam, sample_bam_index, snp_bam, snp_bam_index]
             to_align : snp_fastq
                 return [meta, sample_bam, sample_bam_index, snp_fastq]
+            no_snp: true
+                log.warn("No SNP BAM/CRAM/FASTQ files were detected for '${meta.id}'. Skipping the crosscheck fingerprints step for this sample.")
+                return [[id:meta.pool], []]
         }
         .set{ ch_inputs }
 
@@ -144,7 +140,10 @@ workflow SAMPLETRACKING {
         ch_fasta_fai
     )
     ch_crosscheck_metrics_out = PICARD_CROSSCHECKFINGERPRINTS.out.crosscheck_metrics
-    ch_multiqc_files = ch_multiqc_files.mix(PICARD_CROSSCHECKFINGERPRINTS.out.crosscheck_metrics)
+    ch_multiqc_files = ch_multiqc_files.mix(
+        PICARD_CROSSCHECKFINGERPRINTS.out.crosscheck_metrics,
+        ch_inputs.no_snp.unique() // Add pools with no snp data for flow consistency
+    )
 
 
     //
@@ -283,7 +282,11 @@ workflow SAMPLETRACKING {
         .map { files -> [files] }
         .dump(tag: "Summary files for MultiQC", pretty: true)
     ch_multiqc_input = ch_multiqc_files
-        .groupTuple(by: 0)
+        .map { meta, files ->
+            // This is needed to prevent merge key mismatches on pipeline resume
+            tuple([id: meta.id], files)
+        }
+        .groupTuple(size:2) // size 2 for sex check + crosscheck fingerprints
         .combine(ch_summary_files)
         .map { meta, multiqc_files, summary_files ->
             return [meta, (multiqc_files + summary_files).flatten(), multiqc_config.flatten(), multiqc_logo, [], []]