Merge branch 'master' into add_new_module_vt_decompose_blocksub

modules/nf-core/coptr/estimate/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::coptr=1.1.4"

modules/nf-core/coptr/estimate/main.nf

@@ -0,0 +1,47 @@
+process COPTR_ESTIMATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3':
+        'biocontainers/coptr:1.1.4--pyhdfd78af_3' }"
+
+    input:
+    tuple val(meta), path(pkl, stageAs: "coverage_maps/*")
+
+    output:
+    tuple val(meta), path("*.csv"), emit: ptr
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    coptr \\
+        estimate \\
+        $args \\
+        coverage_maps/ \\
+        ptrs.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/coptr/estimate/meta.yml

@@ -0,0 +1,56 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "coptr_estimate"
+description: Calculates peak-to-through ratio (PTR) from metagenomic sequence data
+keywords:
+  - coptr
+  - mapping
+  - ptr
+tools:
+  - "coptr":
+      description: "Accurate and robust inference of microbial growth dynamics from
+        metagenomic sequencing reads."
+      homepage: "https://github.com/tyjo/coptr"
+      documentation: "https://coptr.readthedocs.io/"
+      tool_dev_url: "https://github.com/tyjo/coptr"
+      doi: "10.1101/gr.275533.121"
+      licence: ["GPL v3"]
+      identifier: biotools:coptr
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - pkl:
+        type: file
+        description: Python pickle file containing coverage maps
+        pattern: "*.pkl"
+        ontologies:
+            - edam: "http://edamontology.org/format_4002"
+
+output:
+  - ptr:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.csv":
+          type: file
+          description: CSV table with rows as reference genomes, columns samples and entries as log2 PTR
+          pattern: "*.csv"
+          ontologies:
+              - edam: "http://edamontology.org/format_3752"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@ramirobarrantes"
+maintainers:
+  - "@ramirobarrantes"

modules/nf-core/coptr/estimate/tests/main.nf.test

@@ -0,0 +1,71 @@
+nextflow_process {
+
+    name "Test Process COPTR_ESTIMATE"
+    script "../main.nf"
+    process "COPTR_ESTIMATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "coptr"
+    tag "coptr/extract"
+    tag "coptr/estimate"
+
+    setup {
+        run("COPTR_EXTRACT") {
+            script "../../extract/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:'test_0'],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+    }
+
+    test("coptr estimate from coverage maps file") {
+
+        when {
+            process {
+                """
+                input[0] = COPTR_EXTRACT.out.coverage
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+
+    }
+
+    test("coptr estimate from coverage maps file - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = COPTR_EXTRACT.out.coverage
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+
+    }
+
+
+}

modules/nf-core/coptr/estimate/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "coptr estimate from coverage maps file - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_0"
+                        },
+                        "test_0.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4"
+                ],
+                "ptr": [
+                    [
+                        {
+                            "id": "test_0"
+                        },
+                        "test_0.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T13:46:59.155895"
+    },
+    "coptr estimate from coverage maps file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_0"
+                        },
+                        "ptrs.csv:md5,e94546e830fd9fdcd50e0e6c459f78e5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4"
+                ],
+                "ptr": [
+                    [
+                        {
+                            "id": "test_0"
+                        },
+                        "ptrs.csv:md5,e94546e830fd9fdcd50e0e6c459f78e5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-11-29T18:28:40.680244"
+    }
+}

modules/nf-core/coptr/extract/main.nf

@@ -41,8 +41,7 @@ process COPTR_EXTRACT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        "${task.process}":
-            coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
     END_VERSIONS
     """
 }

modules/nf-core/coptr/extract/tests/main.nf.test.snap

@@ -83,7 +83,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,578f185b99f7f5ba27eb2a9f44c1d6a9"
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
                 ],
                 "coverage": [
                     [
@@ -94,14 +94,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,578f185b99f7f5ba27eb2a9f44c1d6a9"
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-02T19:26:21.856688"
+        "timestamp": "2024-12-03T13:50:47.572605"
     }
 }

modules/nf-core/coptr/merge/main.nf

@@ -42,7 +42,6 @@ process COPTR_MERGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        "${task.process}":
             coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
     END_VERSIONS
     """

modules/nf-core/coptr/merge/tests/main.nf.test.snap

@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,65562945dc1e8f43bfa9a6e244bbcdf2"
+                    "versions.yml:md5,86e7803a1ea080ab5b7911c540dd1370"
                 ],
                 "bam": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,65562945dc1e8f43bfa9a6e244bbcdf2"
+                    "versions.yml:md5,86e7803a1ea080ab5b7911c540dd1370"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-23T14:54:29.748785"
+        "timestamp": "2024-12-03T13:52:20.557882"
     },
     "coptr merge single bam file": {
         "content": [

modules/nf-core/glimpse2/concordance/main.nf

@@ -9,9 +9,7 @@ process GLIMPSE2_CONCORDANCE {
 
     input:
     tuple val(meta), path(estimate), path(estimate_index), path(truth), path(truth_index), path(freq), path(freq_index), path(samples), val(region)
-    tuple val(meta2), path(groups), val(bins), val(ac_bins), val(allele_counts)
-    val(min_val_gl)
-    val(min_val_dp)
+    tuple val(meta2), path(groups), val(bins), val(ac_bins), val(allele_counts), val(min_val_gl), val(min_val_dp)
 
     output:
     tuple val(meta), path("*.error.cal.txt.gz")  , emit: errors_cal
@@ -26,17 +24,23 @@ process GLIMPSE2_CONCORDANCE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args         = task.ext.args          ?: ''
-    def prefix       = task.ext.prefix        ?: "${meta.id}"
-    def samples_cmd  = samples                ? "--samples ${samples}"             : ""
-    def groups_cmd   = groups                 ? "--groups ${groups}"               : ""
-    def bins_cmd     = bins                   ? "--bins ${bins}"                   : ""
-    def ac_bins_cmd  = ac_bins                ? "--ac-bins ${ac_bins}"             : ""
-    def ale_ct_cmd   = allele_counts          ? "--allele-counts ${allele_counts}" : ""
-    def region_str   = region instanceof List ? region.join('\\n')                 : region
+    def args           = task.ext.args          ?: ''
+    def prefix         = task.ext.prefix        ?: "${meta.id}"
+    def samples_cmd    = samples                ? "--samples ${samples}"             : ""
+    def groups_cmd     = groups                 ? "--groups ${groups}"               : ""
+    def bins_cmd       = bins                   ? "--bins ${bins}"                   : ""
+    def ac_bins_cmd    = ac_bins                ? "--ac-bins ${ac_bins}"             : ""
+    def ale_ct_cmd     = allele_counts          ? "--allele-counts ${allele_counts}" : ""
+    def min_val_gl_cmd = min_val_gl             ? "--min-val-gl ${min_val_gl}"       : ""
+    def min_val_dp_cmd = min_val_dp             ? "--min-val-dp ${min_val_dp}"       : ""
+    def region_str     = region instanceof List ? region.join('\\n')                 : region
 
     if (((groups ? 1:0) + (bins ? 1:0) + (ac_bins ? 1:0) + (allele_counts ? 1:0)) != 1) error "One and only one argument should be selected between groups, bins, ac_bins, allele_counts"
 
+    if (args.contains("--gt-val")) {
+        assert !(min_val_gl || min_val_dp) : "If --gt-val is set, --min-val-gl nor --min-val-dp must be set"
+    }
+
     """
     printf '$region_str' > regions.txt
     sed 's/\$/ $freq $truth $estimate/' regions.txt > input.txt
@@ -47,8 +51,8 @@ process GLIMPSE2_CONCORDANCE {
         $bins_cmd \\
         $ac_bins_cmd \\
         $ale_ct_cmd \\
-        --min-val-gl $min_val_gl \\
-        --min-val-dp $min_val_dp \\
+        $min_val_gl_cmd \\
+        $min_val_dp_cmd \\
         --input input.txt \\
         --thread $task.cpus \\
         --output ${prefix}

modules/nf-core/glimpse2/concordance/meta.yml

@@ -79,12 +79,12 @@ input:
         description: |
           Default allele count bins used for rsquared computations.
           AN field must be defined in the frequency file.
-  - - min_val_gl:
+    - min_val_gl:
         type: float
         description: |
           Minimum genotype likelihood probability P(G|R) in validation data.
           Set to zero to have no filter of if using –gt-validation
-  - - min_val_dp:
+    - min_val_dp:
         type: integer
         description: |
           Minimum coverage in validation data.