Feature/giab eval refactor

main.nf

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+/*
+ * not actually used - just a placeholder
+ */

modules/UMCUGenetics/utils/editsummaryfilehappy/main.nf

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+process UTILS_EDITSUMMARYFILEHAPPY {
+    tag "${meta.id}"
+    label 'process_low'
+
+    input:
+    tuple val(meta), path(summary_csv)
+
+    output:
+    path("*_INDEL_PASS.summary.csv"), emit: indel_pass_csv
+    path("*_INDEL_ALL.summary.csv"), emit: indel_all_csv
+    path("*_SNP_PASS.summary.csv"), emit: snp_pass_csv
+    path("*_SNP_ALL.summary.csv"), emit: snp_all_csv
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+        # Add samplenames as columns (header and row values) at start of line
+        sed '1s/^/samples,sample_truth,sample_query,/; 2,\$s/^/${meta.truth}_${meta.query},${meta.truth},${meta.query},/' ${summary_csv} > ${summary_csv}.tmp
+
+        # Split file including header (first line)
+        awk -F',' 'FNR==1{hdr=\$0;next} {
+            print hdr>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv";
+            print \$0>>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv"
+        }' ${summary_csv}.tmp
+
+        # Remove tmp files
+        rm ${summary_csv}.tmp
+    """
+
+    stub:
+    """
+    touch ${meta.truth}_${meta.query}_INDEL_PASS.summary.csv
+    touch ${meta.truth}_${meta.query}_INDEL_ALL.summary.csv
+    touch ${meta.truth}_${meta.query}_SNP_PASS.summary.csv
+    touch ${meta.truth}_${meta.query}_SNP_ALL.summary.csv
+    """
+
+
+}

modules/UMCUGenetics/utils/editsummaryfilehappy/meta.yml

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+name: editsummaryfilehappy
+description: Reformat the happy summary file for GIABEval
+keywords:
+  - giab
+  - GIABEval
+  - utils
+
+tools:
+  - bash:
+      description: |
+        Util process, using only bash
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information it should have the keys [id: '', 'query', 'truth']
+    - summary_csv:
+        type: file
+        description: summary output csv from happy
+output:
+  indel_pass_csv:
+    - "*_INDEL_PASS.summary.csv":
+        type: file
+        description: "INDELs that pass the criteria"
+  indel_all_csv:
+    - "*_INDEL_ALL.summary.csv":
+        type: file
+        description: "All indels"
+  snp_pass_csv:
+    - "*_SNP_PASS.summary.csv":
+        type: file
+        description: "SNPs that pass the criteria"
+  snp_all_csv:
+    - "*_SNP_ALL.summary.csv":
+        type: file
+        description: "All SNPs"  
+
+authors:
+  - "@ellendejong"
+  - "@melferink"
+

modules/UMCUGenetics/utils/editsummaryfilehappy/tests/main.nf.test

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+nextflow_process {
+    name "Test UTILS_EDITSUMMARYFILEHAPPY"
+    script "../main.nf"
+    process "UTILS_EDITSUMMARYFILEHAPPY"
+
+    tag "modules"
+    tag "modules_umcugenetics"
+    tag "happy"
+
+    test("stub") {
+        options "-stub"
+        when{
+            process{
+                """
+                input[0] = [
+                    [id: 'test', truth: 'truthsample', query: "querysample"], // meta map
+                    file("demo_summary.csv")
+                ]
+                """
+            }
+        }
+        then {
+            assert process.success
+        }
+    }
+}

nf-test.config

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+config {
+    // location for all nf-tests
+    testsDir = "."
+
+    // nf-test directory including temporary files for each test
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile = "tests/config/nf-test.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile = ""
+
+}

tests/config/nextflow.config

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+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    singularity_pull_docker_container = false
+    test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+}
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '16.GB',
+        time: '1.h'
+    ]
+}
+
+profiles {
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        singularity.registry = 'quay.io'
+    }
+
+    conda {
+        conda.enabled  = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    mamba {
+        conda.enabled  = true
+        conda.useMamba = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    micromamba {
+        conda.enabled  = true
+        conda.useMicromamba = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    podman {
+        podman.enabled = true
+        podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+        podman.registry = 'quay.io'
+    }
+
+    docker {
+        docker.enabled = true
+        docker.fixOwnership = true
+        docker.runOptions = '--platform=linux/amd64'
+        docker.registry = 'quay.io'
+    }
+}
+
+// Load test_data.config containing paths to test data
+includeConfig 'test_data.config'
+
+manifest {
+    nextflowVersion = '!>=24.10.2'
+}

tests/config/nf-test.config

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+params {
+    publish_dir_mode                  = "copy"
+    singularity_pull_docker_container = false
+    test_data_base                    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+    modules_testdata_base_path        = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+}
+
+process {
+    cpus   = 2
+    memory = '4.GB'
+    time   = '2.h'
+}
+
+profiles {
+    conda {
+        conda.enabled           = true
+        conda.channels          = ['conda-forge', 'bioconda']
+        apptainer.enabled       = false
+    }
+    mamba {
+        conda.enabled           = true
+        conda.useMamba          = true
+    }
+    micromamba {
+        conda.enabled           = true
+        conda.useMicromamba     = true
+    }
+    docker {
+        docker.enabled          = true
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+    docker_self_hosted {
+        docker.enabled          = true
+        docker.fixOwnership     = true
+        docker.runOptions       = '--platform=linux/amd64'
+    }
+    arm64 {
+        process.arch            = 'arm64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/arm64'
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+    singularity {
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+    }
+    podman {
+        podman.enabled          = true
+        podman.runOptions       = "--runtime crun --platform linux/x86_64 --systemd=always"
+    }
+    shifter {
+        shifter.enabled         = true
+    }
+    charliecloud {
+        charliecloud.enabled    = true
+    }
+    apptainer {
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    gitpod {
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
+    }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
+}
+
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Increase time available to build Conda environment
+conda { createTimeout = "120 min" }
+
+// Load test_data.config containing paths to test data
+includeConfig 'test_data.config'
+
+manifest {
+    nextflowVersion = '!>=24.10.2'
+}