Merge branch 'nf-core:master' into gzrt

nf-core · Dec 19, 2024 · 6304d06 · 6304d06
2 parents 3f2a52b + cc217b9
commit 6304d06
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Showing 13 changed files with 129 additions and 76 deletions.
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/flye/main.nf b/modules/nf-core/flye/main.nf
@@ -4,8 +4,8 @@ process FLYE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/flye:2.9.5--eb07d7b7094f222c' :
-        'community.wave.seqera.io/library/flye:2.9.5--0221998e9c3ec606' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fa1c1e961de38d24cf36c424a8f4a9920ddd07b63fdb4cfa51c9e3a593c3c979/data' :
+        'community.wave.seqera.io/library/flye:2.9.5--d577924c8416ccd8' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/metabat2/metabat2/environment.yml b/modules/nf-core/metabat2/metabat2/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::metabat2=2.15
+  - bioconda::metabat2=2.17
diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf
@@ -4,8 +4,8 @@ process METABAT2_METABAT2 {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
-        'biocontainers/metabat2:2.15--h986a166_1' }"
+        'https://depot.galaxyproject.org/singularity/metabat2:2.17--hd498684_0' :
+        'biocontainers/metabat2:2.17--hd498684_0' }"
 
     input:
     tuple val(meta), path(fasta), path(depth)
@@ -24,15 +24,16 @@ process METABAT2_METABAT2 {
     script:
     def args             = task.ext.args   ?: ''
     def prefix           = task.ext.prefix ?: "${meta.id}"
-    def decompress_depth = depth           ? "gzip -d -f $depth"    : ""
-    def depth_file       = depth           ? "-a ${depth.baseName}" : ""
+    def clean_depth      = depth.toString() - ~/\.gz$/
+    def decompress_depth = (depth && depth.toString() != clean_depth) ? "gzip -d -f $depth" : ""
+    def depth_input      = depth ? "-a ${clean_depth}" : ""
     """
     $decompress_depth
 
     metabat2 \\
-        $args \\
+        ${args} \\
         -i $fasta \\
-        $depth_file \\
+        ${depth_input} \\
         -t $task.cpus \\
         --saveCls \\
         -o ${prefix}

diff --git a/modules/nf-core/metabat2/metabat2/tests/main.nf.test b/modules/nf-core/metabat2/metabat2/tests/main.nf.test
@@ -7,10 +7,35 @@ nextflow_process {
 
     tag "modules"
     tag "modules_nfcore"
+    tag "gunzip"
     tag "metabat2"
     tag "metabat2/metabat2"
     tag "metabat2/jgisummarizebamcontigdepths"
 
+    setup {
+        run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") {
+            script "../../jgisummarizebamcontigdepths/main.nf"
+            process {
+                """
+                input[0] = [
+                                [id: 'test', single_end: false],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                            ]
+                """
+            }
+        }
+
+        run("GUNZIP") {
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth
+                """
+            }
+        }
+    }
+
     test("sarscov2 - genome - fasta") {
 
         when {
@@ -36,28 +61,35 @@ nextflow_process {
 
     test("sarscov2 - genome - fasta - depths") {
 
-        setup {
-            run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") {
-                script "../../jgisummarizebamcontigdepths/main.nf"
-                process {
-                    """
-                    input[0] = [
-                                    [id: 'test', single_end: false],
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                                ]
-                    """
-                }
+        when {
+            process {
+                """
+                input[0] = Channel
+                            .fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                            .map { it -> [[ id:'test', single_end:false ], it] }
+                            .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+                """
             }
         }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.membership[0][1]).name).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - depths uncompressed") {
+
         when {
             process {
                 """
                 input[0] = Channel
                             .fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             .map { it -> [[ id:'test', single_end:false ], it] }
-                            .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+                            .join(GUNZIP.out.gunzip)
                 """
             }
         }