Feature/allow nextflow run usage

.github/pull_request_template.md

@@ -10,18 +10,16 @@ Thank you for submitting this PR.
 
 Before merge:
 
-* The PR must be reviewed by one of the team members.
+* A PR must be reviewed by one of the team members.
 
-* Please check if anything in the Readme must be adjusted, or added (development-setup, production-setup, user-guide).
+* Please check if anything in the documentation must be adjusted, or added (development-setup, production-setup, user-guide).
 
-* PRs with new modules or workflow interfaces must include tests according to the developer [guidelines](https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta-omics-toolkit/master.html#developer_guidelines).
+* PRs with new modules or workflow interfaces must include tests according to the developer [guidelines](https://metagenomics.github.io/metagenomics-tk/latest/developer_guidelines/).
 
-* The new code is readable, well commented and should adhere to our developer [guidelines](https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta-omics-toolkit/master.html#developer_guidelines).
+* The new code is readable, well commented and should adhere to our developer [guidelines](https://metagenomics.github.io/metagenomics-tk/latest/developer_guidelines/).
 
 * Before merging it must be checked if a squash of commits is required.
 
 
 
 
-
-

.github/workflows/workflow_modules.yml

@@ -6,7 +6,7 @@ concurrency:
 env:
   WORK_DIR: "/vol/spool/${{ github.ref_name }}"
   PROFILE: "slurm"
-  PR_NUMBER: ${{ github.event.number }}
+  PR_NUMBER: ${{ github.event.pull_request.number }}
   EMGB_KEGG_DB: "/vol/spool/emgb/annotatedgenes2json_db_kegg-mirror-2022-12" 
   EMGB_DB_TITLES: "/vol/spool/emgb/uniref90.titles.tsv.gz"
 jobs:
@@ -244,7 +244,8 @@ jobs:
     runs-on: [ self-hosted, slurm]
     needs: [codePolicy]
     steps:
-      - name: Test Dereplication
+      - uses: actions/checkout@v4
+      - name: Test Quickstart
         run: |
           bash ./scripts/test_quickstart.sh || exit 1
 
@@ -572,15 +573,15 @@ jobs:
           VERSION=$(sort VERSIONS.txt | tail -n 1)
           OUTPUT=outputEasy
           bash ./scripts/test_settings.sh \
-          " --preset --scratch /vol/scratch --input.paired.path test_data/fullPipeline/reads_split.tsv --highmemLarge=28,2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT} " \
+          " --preset --template default/fullPipeline_illumina_nanpore.yml --scratch /vol/scratch --input.paired.path test_data/fullPipeline/reads_split.tsv --highmemLarge=28,2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT} " \
           "   " "${WORK_DIR}" ${PROFILE} ${VERSION} "preset" || exit 1
           bash ./scripts/check_parameter.sh ${OUTPUT} || exit 1
       - name: Test whether settings in default mode can be updated
         run: |
           VERSION=$(sort VERSIONS.txt | tail -n 1)
           OUTPUT=outputDefault
           bash ./scripts/test_settings.sh \
-          "  --scratch /vol/scratch  --resources.highmemLarge.memory=2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT}  " \
+          "  --scratch /vol/scratch --template default/fullPipeline_illumina_nanpore.yml --resources.highmemLarge.memory=2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT}  " \
           "" "${WORK_DIR}" ${PROFILE} ${VERSION} "" || exit 1
           bash ./scripts/check_parameter.sh ${OUTPUT} || exit 1
 

docs/quickstart.md

@@ -8,9 +8,8 @@ You will need at least 250 GB of disk space. The disk were your docker images an
 ## Requirements
 
 1. docker: Install Docker by following the official Docker installation [instructions](https://docs.docker.com/engine/install/ubuntu/).
-2. make: You can install make on Ubuntu via `sudo apt install make` 
-3. java: In order to run Nextflow you need to install Java on your machine which can be achieved via `sudo apt install default-jre`
-4. Resources:  
+2. make: You can install make on Ubuntu via `sudo apt install make`.
+3. java: In order to run Nextflow you need to install Java on your machine which can be achieved via `sudo apt install default-jre`.
 
 ## Preparation
 

modules/assembly/shortReadAssembler.nf

@@ -373,11 +373,11 @@ workflow _wCalculateMegahitResources {
          modelType = Channel.empty()
          if(params.steps.containsKey("assembly") && params.steps.assembly.containsKey("megahit") \
 		&& params?.steps?.assembly?.megahit?.additionalParams.contains("meta-sensitive")){
-         	model = Channel.value(file("${baseDir}/models/assembler/megahit/sensitive.pkl"))
+         	model = Channel.value(file("${projectDir}/models/assembler/megahit/sensitive.pkl"))
 		modelType = Channel.value("sensitive")
 	 } else {
 		modelType = Channel.value("default")
-         	model = Channel.value(file("${baseDir}/models/assembler/megahit/default.pkl"))
+         	model = Channel.value(file("${projectDir}/models/assembler/megahit/default.pkl"))
 	 }
 
          resourceType.predict | join(nonpareil | splitCsv(header: true, sep: '\t') \

nextflow.config

@@ -46,13 +46,45 @@ if("dry-run" in params.keySet()){
 	System.out.println("Dry-run is enabled!")
 }
 
+def configUrlString = "https://raw.githubusercontent.com/metagenomics/metagenomics-tk/refs/tags/" + manifest.version + "/default/fullPipeline_illumina_nanpore.yml"
 
-template = (params.containsKey("template") && params.containsKey("preset")) ?  params.template : "default/fullPipeline_illumina_nanpore.yml"
+/*
+*
+* Check if --preset is set and/or a template for a Toolkit configuration file is provided.
+* Depending on the setting the corresponding configuration file is loaded.
+*
+*/
+def loadYAML(configUrlString){
+  if((params.containsKey("template") && params.containsKey("preset"))){
+    return new Yaml().load(new File(params.template))
+  }
+  if(params.containsKey("preset")){
+    try {
+      // Step 1: Fetch the remote YAML content
+      def url = new URL(configUrlString)
+      def connection = url.openConnection()
+      connection.setRequestMethod('GET')
+
+      if (connection.responseCode == HttpURLConnection.HTTP_OK) {
+        def reader = connection.inputStream.withReader { it.text }
+
+        // Step 2: Parse the YAML content
+        return new Yaml().load(reader)
+
+      } else {
+        println "GET request not worked, response code: ${connection.responseCode}"
+        System.exit(1)
+      }
+    } catch (Exception e) {
+      e.printStackTrace()
+    }
+  }
 
-defaultYmlFile = new File("${baseDir}/" + template)
-preLoadYML = new Yaml().load(defaultYmlFile.text)
+  return null
+}
 
 
+preLoadYML = loadYAML(configUrlString)
 
 
 /*
@@ -64,15 +96,17 @@ def getPresetSteps(){
    disableModules = ["metabolomics", "annotation", "fragmentRecruitment"]
    steps = preLoadYML["steps"]
 
+
    stepsKeys = steps.keySet()
 
    def stepsMap = [:]
 
    System.out.println(PRETTY_SEPARATOR)
    System.out.println("The following modules will be executed:\n")
+
    for(step in stepsKeys){
+
      if(!params.keySet().contains("no-" + step) && ! disableModules.contains(step)){
-       System.out.println(step)
        stepsMap[step] = steps[step]
      }
    }
@@ -543,7 +577,7 @@ profiles {
         docker {
            fixOwnership = true
            enabled = true
-         }
+        }
 
         process {
            cache = 'lenient'