Merge branch 'master' into nf-test_phispy

* master: Migrate meryl unionsum nftest (#5404) Adding Fast epistasis module (#5389) corrected bug in asereadcounter (#5403) Meryl count and meryl histogram migration to nf-test (#5401)
nf-core · Mar 27, 2024 · 251f94d · 251f94d
2 parents b4ee797 + b7f584e
commit 251f94d
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diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf
@@ -8,11 +8,10 @@ process GATK4_ASEREADCOUNTER {
         'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index)
-    tuple val(meta2), path(vcf), path(tbi)
-    tuple val(meta3), path(fasta)
-    tuple val(meta4), path(fai)
-    tuple val(meta5), path(dict)
+    tuple val(meta),  path(bam), path(bai), path(vcf), path(tbi)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
     path intervals
 
     output:
@@ -39,7 +38,7 @@ process GATK4_ASEREADCOUNTER {
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         ASEReadCounter \\
         --output ${prefix}_ase.csv \\
-        --input ${input} \\
+        --input ${bam} \\
         --variant ${vcf} \\
         $reference_command \\
         $intervals_command \\

diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test b/modules/nf-core/gatk4/asereadcounter/main.nf.test
@@ -16,26 +16,23 @@ nextflow_process {
                 input[0] = [ 
                     [ id:'test' ], // meta map
                     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)
-                ]
-                input[1] = [
-                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[2] = [
+                input[1] = [
                     [ id:'reference' ], // meta map
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'reference' ], // meta map
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'reference' ], // meta map
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
                 ]
-                input[5] = [ 
+                input[4] = [ 
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
                 ]
                 """

diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml
@@ -29,11 +29,6 @@ input:
       type: file
       description: index file for input file
       pattern: "*.{bai,crai}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. `[ id:'reference' ]`
   - vcf:
       type: file
       description: VCF file
@@ -42,7 +37,7 @@ input:
       type: file
       description: index file for VCF file
       pattern: "*.{vcf.gz.tbi}"
-  - meta3:
+  - meta2:
       type: map
       description: |
         Groovy Map containing reference information
@@ -51,7 +46,7 @@ input:
       type: file
       description: fasta file
       pattern: "*.{fasta,fa}"
-  - meta4:
+  - meta3:
       type: map
       description: |
         Groovy Map containing reference information
@@ -60,7 +55,7 @@ input:
       type: file
       description: fasta index file
       pattern: "*.{fai}"
-  - meta5:
+  - meta4:
       type: map
       description: |
         Groovy Map containing reference information

diff --git a/modules/nf-core/genomescope2/tests/main.nf.test b/modules/nf-core/genomescope2/tests/main.nf.test
@@ -20,6 +20,7 @@ nextflow_process {
                     [ id: 'test', single_end: true ], // meta map
                     file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true )
                 ])
+                input[1] = Channel.value(21)
                 """
             }
         }
@@ -28,6 +29,7 @@ nextflow_process {
             process {
                 """
                 input[0] = MERYL_COUNT.out.meryl_db
+                input[1] = Channel.value(21)
                 """
             }
         }

diff --git a/modules/nf-core/genomescope2/tests/nextflow.config b/modules/nf-core/genomescope2/tests/nextflow.config
@@ -1,7 +1,4 @@
 process {
-    withName: 'MERYL.*' {
-        ext.args = 'k=21'
-    }
     withName: 'GENOMESCOPE2' {
         ext.args = '-k 21 -p 1 --fitted_hist'
     }

diff --git a/modules/nf-core/meryl/count/environment.yml b/modules/nf-core/meryl/count/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::meryl=1.3
+  - bioconda::meryl=1.4.1
diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf
@@ -4,11 +4,12 @@ process MERYL_COUNT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
-        'biocontainers/meryl:1.3--h87f3376_1' }"
+        'https://depot.galaxyproject.org/singularity/meryl:1.4.1--h4ac6f70_0':
+        'biocontainers/meryl:1.4.1--h4ac6f70_0' }"
 
     input:
     tuple val(meta), path(reads)
+    val kvalue
 
     output:
     tuple val(meta), path("*.meryldb"), emit: meryl_db
@@ -23,6 +24,7 @@ process MERYL_COUNT {
     """
     for READ in $reads; do
         meryl count \\
+            k=$kvalue \\
             threads=$task.cpus \\
             $args \\
             $reads \\
@@ -34,4 +36,18 @@ process MERYL_COUNT {
         meryl: \$( meryl --version |& sed 's/meryl //' )
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    for READ in $reads; do
+        touch read.\${READ%.f*}.meryldb
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml
@@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
   - k-mer
   - count
+  - reference-free
 tools:
   - "meryl":
       description: "A genomic k-mer counter (and sequence utility) with nice features. "
       homepage: "https://github.com/marbl/meryl"
       documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
       tool_dev_url: "https://github.com/marbl/meryl"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
@@ -21,6 +22,9 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - kvalue:
+      type: integer
+      description: An integer value of k to use as the k-mer value.
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/meryl/count/tests/main.nf.test b/modules/nf-core/meryl/count/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process MERYL_COUNT"
+    script "../main.nf"
+    process "MERYL_COUNT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "meryl"
+    tag "meryl/count"
+
+    test("bacteroides_fragilis - fastq") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id: 'test', single_end: true ], // meta map
+                    file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true )
+                ])
+                input[1] = Channel.value(21)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("bacteroides_fragilis - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id: 'test', single_end: true ], // meta map
+                    file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true )
+                ])
+                input[1] = Channel.value(21)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}