Update worklow output definitions to 25.04.0 (#115)

* update workflow-output-defs to 25.04.0

* update tests

* update changelog

Author: nvnieuwk

.github/workflows/ci.yml

@@ -21,15 +21,15 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test_all:
+  test:
     name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }}
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/structural') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.0"
+          - "25.04.0"
           - "latest-everything"
         test:
           - "pipeline_sv"

CHANGELOG.md

@@ -19,10 +19,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 4. Updated to nf-core template v3.2.0
 5. Fixed language server errors
 6. Removed the old output publishing code and used the new workflow output definitions instead
-7. Bumped the minimal nextflow version to 24.10.0
+7. Bumped the minimal nextflow version to 25.04.0
 8. VCFanno will now run when `--vcfanno_toml` has been given and `--annotate` has not been given. You still need to supply `--annotate` to get the full annotation, but this can be used check for common variants without having to perform full annotation.
 9. Changed the `--annotations_filter` parameter to a `--filter` parameter. This parameter takes an argument of `bcftools filter` to filter the resulting VCFs.
 10. Removed the `--delly_sv_types` parameter.
+11. Moved all `wisecondorx` and `qdnaseq` outputs to a separate directory in each sample output.
 
 ### `Fixed`
 

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/structural/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/structural/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)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

main.nf

@@ -128,74 +128,68 @@ workflow {
     )
 
     publish:
-    STRUCTURAL.out.caller_vcfs      >> 'caller_vcfs'
-    STRUCTURAL.out.sample_vcfs      >> 'sample_vcfs'
-    STRUCTURAL.out.family_vcfs      >> 'family_vcfs'
-    STRUCTURAL.out.qdnaseq_out      >> 'qdnaseq_out'
-    STRUCTURAL.out.wisecondorx_out  >> 'wisecondorx_out'
-    STRUCTURAL.out.bedpe            >> 'bedpe'
-    STRUCTURAL.out.multiqc_report   >> 'multiqc'
-    STRUCTURAL.out.multiqc_data     >> 'multiqc_data'
+    caller_vcfs     = STRUCTURAL.out.caller_vcfs
+    sample_vcfs     = STRUCTURAL.out.sample_vcfs
+    family_vcfs     = STRUCTURAL.out.family_vcfs
+    qdnaseq_out     = STRUCTURAL.out.qdnaseq_out
+    wisecondorx_out = STRUCTURAL.out.wisecondorx_out
+    bedpe           = STRUCTURAL.out.bedpe
+    multiqc         = STRUCTURAL.out.multiqc_report
+    multiqc_data    = STRUCTURAL.out.multiqc_data
 
 }
 
 output {
-    'caller_vcfs' {
+    caller_vcfs {
         enabled params.output_callers
-        path { meta, vcf, _tbi -> { file ->
-            if(file == vcf.name) {
-                return "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz"
-            }
-            return "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz.tbi"
-        } }
+        path { meta, vcf, tbi ->
+            vcf >> "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz"
+            tbi >> "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz.tbi"
+        }
     }
-    'sample_vcfs' {
-        path { meta, vcf, _tbi -> { file ->
+    sample_vcfs {
+        path { meta, vcf, tbi ->
             def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            if(file == vcf.name) {
-                return "${base}.vcf.gz"
-            }
-            return "${base}.vcf.gz.tbi"
-        } }
+            vcf >> "${base}.vcf.gz"
+            tbi >> "${base}.vcf.gz.tbi"
+        }
     }
-    'family_vcfs' {
-        path { meta, vcf, _tbi -> { file ->
+    family_vcfs {
+        path { meta, vcf, tbi ->
             def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            if(file == vcf.name) {
-                return "${base}.vcf.gz"
-            }
-            return "${base}.vcf.gz.tbi"
-        } }
+            vcf >> "${base}.vcf.gz"
+            tbi >> "${base}.vcf.gz.tbi"
+        }
     }
-    'qdnaseq_out' {
-        path { meta, _bed -> { file ->
-            if(file == "statistics.out") {
-                return "${meta.id}/${meta.id}.qdnaseq.statistics.out"
-            }
-            def new_name = file.replaceFirst(meta.id, "${meta.id}.qdnaseq")
-            return "${meta.id}/${new_name}"
-        } }
+    qdnaseq_out {
+        path { meta, _bed_qdnaseq -> "$meta.id/qdnaseq/"
+            // def base_suffix = bed_qdnaseq.name.replace(meta.id, "${meta.id}.qdnaseq")
+            // bed_qdnaseq >> bed_qdnaseq.name == "statistics.out" ?
+            //     "${meta.id}/${meta.id}.qdnaseq.statistics.out" :
+            //     "${meta.id}/${base_suffix}"
+        }
     }
-    'wisecondorx_out' {
-        path { meta, _bed -> { file ->
-            if(file.endsWith(".png")) {
-                return "${meta.id}/${meta.id}.wisecondorx.${file}"
-            }
-            def new_name = file.replaceFirst(meta.id, "${meta.id}.wisecondorx")
-            return "${meta.id}/${new_name}"
-        } }
+    wisecondorx_out {
+        path { meta, _bed -> "$meta.id/wisecondorx/"
+            // if(bed.name.endsWith(".png")) {
+            //     bed >> "${meta.id}/${meta.id}.wisecondorx.${bed.name}"
+            // } else {
+            //     def new_name = bed.name.replaceFirst(meta.id, "${meta.id}.wisecondorx")
+            //     bed >> "${meta.id}/${new_name}"
+            // }
+        }
     }
-    'bedpe' {
-        path { meta, _bedpe -> { file ->
+    bedpe {
+        path { meta, bedpe ->
             def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            return "${base}.bedpe"
-        } }
+            bedpe >> "${base}.bedpe"
+        }
     }
-    'multiqc' {
-        path { _report -> { _file -> "multiqc/multiqc_report.html"}}
+    multiqc {
+        path { "multiqc/" }
     }
-    'multiqc_data' {
-        path { _folder -> { _file -> "multiqc/multiqc_data"}}
+    multiqc_data {
+        path { "multiqc/" }
     }
 }
 

nextflow.config

@@ -279,7 +279,7 @@ manifest {
     description     = """A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads."""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=24.10.0'
+    nextflowVersion = '!>=25.04.0'
     version         = '0.3.0dev'
     doi             = ''
 }