Ben made me do this (+ nf-schema migration) (#98)

* ben made me do this part 1

* ben made me do more stuff

* ben made me refactor my configs and tests

* i made myself add nf-schema

* possible fix for the tests

* bump nextflow versions to enable resourceLimits

* fix wcx snap

* fix qdnaseq snap

* readlines > readLines

* fix annot snap

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.0"
           - "latest-everything"
         test:
           - "pipeline_sv"
@@ -70,7 +70,7 @@ jobs:
 
       - name: Install nf-test
         run: |
-          conda install -c bioconda nf-test==0.8.4
+          conda install -c bioconda nf-test
 
       - name: Run pipeline with test data
         run: |

CHANGELOG.md

@@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changes`
 
+1. Updated the pipeline to be compatible with future nextflow updates
+2. Removed the `max_cpus`, `max_memory` and `max_time` parameter in favor of the new built-in `resourceLimits`
+3. Replaced `nf-validation` with `nf-schema`
+
 ### `Fixed`
 
 1. Fail the pipeline when the sex determination failed. This will now prompt the user to add the sex to the samplesheet so the pipeline doesn't do any wrong assumptions

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)
 [![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%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.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/)

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-cmgg/structural/master/assets/schema_input.json",
     "title": "nf-cmgg/structural pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

conf/base.config

@@ -10,47 +10,40 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1    * task.attempt }
+    memory = { 8.GB * task.attempt }
+    time   = { 4.h  * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                     }
+        memory = { 8.GB * task.attempt   }
+        time   = { 4.h  * task.attempt   }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt  }
+        memory = { 16.GB * task.attempt  }
+        time   = { 4.h   * task.attempt  }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 4     * task.attempt  }
+        memory = { 32.GB * task.attempt  }
+        time   = { 8.h   * task.attempt  }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 8     * task.attempt  }
+        memory = { 64.GB * task.attempt  }
+        time   = { 16.h  * task.attempt  }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt  }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
@@ -59,7 +52,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }

conf/empty_genomes.config

@@ -0,0 +1 @@
+params.genomes = [:]

conf/empty_test_data.config

@@ -0,0 +1 @@
+params.test_data = [:]