Merge branch 'master' into star-update-module

nf-core · Oct 7, 2024 · 20757b2 · 20757b2
2 parents b506e13 + f8ee14d
commit 20757b2
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diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
@@ -4,8 +4,8 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
@@ -4,8 +4,8 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
@@ -4,8 +4,8 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
@@ -4,8 +4,8 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

diff --git a/modules/nf-core/longphase/haplotag/main.nf b/modules/nf-core/longphase/haplotag/main.nf
@@ -24,8 +24,8 @@ process LONGPHASE_HAPLOTAG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sv_file = params.svs ? "--sv-file ${svs}" : ""
-    def mod_file = params.mods ? "--mod-file ${mods}" : ""
+    def sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
 
     """
     longphase \\

diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
@@ -119,15 +119,15 @@
                 "@RG\tID:test\tSM:test",
                 "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz",
                 "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index",
-                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam "
+                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam --sv-file NA24385_sv.vcf.gz "
             ],
             "721264eb2824a3146b331f2532d10180"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T09:13:39.901419316"
+        "timestamp": "2024-10-04T13:39:33.50395694"
     },
     "[ bam, bai, snps, [], [] ], fasta, fai - log & cram": {
         "content": [

diff --git a/modules/nf-core/longphase/phase/main.nf b/modules/nf-core/longphase/phase/main.nf
@@ -24,8 +24,8 @@ process LONGPHASE_PHASE {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sv_file = params.svs ? "--sv-file ${svs}" : ""
-    def mod_file = params.mods ? "--mod-file ${mods}" : ""
+    def sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
 
     def bamList = []
     for (file in bam) {

diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test.snap b/modules/nf-core/longphase/phase/tests/main.nf.test.snap
@@ -40,7 +40,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
                     ]
                 ],
                 "1": [
@@ -51,7 +51,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
                     ]
                 ],
                 "versions": [
@@ -60,10 +60,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:14:39.961315592"
+        "timestamp": "2024-10-04T13:37:16.921910004"
     },
     "[ bam x2, bai x2, snps, svs, [] ], fasta, fai": {
         "content": [
@@ -73,7 +73,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687"
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
                     ]
                 ],
                 "1": [
@@ -84,7 +84,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687"
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
                     ]
                 ],
                 "versions": [
@@ -93,10 +93,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:15:07.970597495"
+        "timestamp": "2024-10-04T13:37:23.41768963"
     },
     "[ bam, bai, snps, [], [] ], fasta, fai - stub": {
         "content": [

diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::motus=3.1.0
diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
@@ -0,0 +1,53 @@
+process MOTUS_PREPLONG {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0':
+        'biocontainers/motus:3.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.gz"), emit: out
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def refdb = db ? "-db ${db}" : ""
+
+    """
+    motus \\
+        prep_long \\
+        $args \\
+        -i $reads \\
+        $refdb \\
+        -t $task.cpus \\
+        -o ${prefix}.gz \\
+        2> >(tee ${prefix}.log >&2)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo '' | gzip > ${prefix}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
@@ -0,0 +1,52 @@
+name: "motus_preplong"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "Marker gene-based operational taxonomic unit (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1186/s40168-022-01410-z"
+      licence: ["GPL v3"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
+        pattern: "*.{gz}"
+  - - db:
+        type: directory
+        description: |
+          mOTUs database downloaded by `motus downloadDB`
+          pattern: "db_mOTU/"
+output:
+  - out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.gz":
+          type: file
+          description: converted file (gzipped), ready to be used by motus profile
+          pattern: "*.gz"
+  - versions:
+      - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@sofstam"
+maintainers:
+  - "@sofstam"
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process MOTUS_PREPLONG"
+    script "../main.nf"
+    process "MOTUS_PREPLONG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "motus"
+    tag "motus/downloaddb"
+    tag "motus/preplong"
+
+    setup {
+        run("MOTUS_DOWNLOADDB") {
+            script "modules/nf-core/motus/downloaddb/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+
+    }
+
+}