Merge branch 'master' into deepv

nf-core · Jan 9, 2025 · 8b902e8 · 8b902e8
2 parents 98b1c2f + f46e02b
commit 8b902e8
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diff --git a/modules/nf-core/affy/justrma/templates/affy_justrma.R b/modules/nf-core/affy/justrma/templates/affy_justrma.R
@@ -54,7 +54,7 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL){
 #' Install the right CDF for a given cel file
 #'
 #' @param celfile A valid path to a CEL file
-#' @param annotation Boolean indication wheter to install the annotation
+#' @param annotation Boolean indication whether to install the annotation
 #'        package
 #'
 #' @return output The CDF environment or a list detailing the failed locations.

diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml
@@ -37,7 +37,7 @@ input:
   - - config:
         type: file
         description: |
-          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
         pattern: "*.yaml"
 output:
   - gff:

diff --git a/modules/nf-core/agat/spmergeannotations/meta.yml b/modules/nf-core/agat/spmergeannotations/meta.yml
@@ -31,7 +31,7 @@ input:
         type: file
         description: |
           Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,
-          otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml
+          otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml
           locally type: "agat config --expose". The --config option gives you the possibility to use your
           own AGAT config file (located elsewhere or named differently).
         pattern: "*.yaml"

diff --git a/modules/nf-core/agrvate/meta.yml b/modules/nf-core/agrvate/meta.yml
@@ -33,12 +33,12 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${fasta.baseName}-results/${fasta.baseName}-summary.tab:
           type: file
-          description: A summary of the agrvate assessement
+          description: A summary of the agrvate assessment
           pattern: "*-summary.tab"
   - results_dir:
       - ${fasta.baseName}-results:
           type: directory
-          description: Results of the agrvate assessement
+          description: Results of the agrvate assessment
           pattern: "*-results"
   - versions:
       - versions.yml:

diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml
@@ -155,7 +155,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - amp_ref_database/*.clean.fasta:
           type: file
-          description: AMP reference database fasta file, cleaned of diamond-uncompatible
+          description: AMP reference database fasta file, cleaned of diamond-incompatible
             characters.
           pattern: "/amp_ref_database/*.clean.fasta"
   - results_db_tsv:

diff --git a/modules/nf-core/ampcombi2/parsetables/meta.yml b/modules/nf-core/ampcombi2/parsetables/meta.yml
@@ -176,7 +176,6 @@ output:
       - amp_${opt_amp_db}_database/*.fasta:
           type: file
           description: AMP reference database fasta file in clean format.
-            characters.
           pattern: "/amp_*_database/*.fasta"
   - db_mmseqs:
       - meta:

diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)

diff --git a/modules/nf-core/annotsv/installannotations/main.nf b/modules/nf-core/annotsv/installannotations/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations

diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml
@@ -36,13 +36,13 @@ output:
       - protein_domains*${genome}*.gff3:
           type: file
           description: Protein domain annotations
-          patter: "*.gff3"
+          pattern: "*.gff3"
   - known_fusions:
       - known_fusions*${genome}*.tsv.gz:
           type: file
           description: Arriba is more sensitive to those fusions to improve the detection
             rate of expected or highly relevant events, such as recurrent fusions
-          patter: "*.tsv.gz"
+          pattern: "*.tsv.gz"
   - versions:
       - versions.yml:
           type: file

diff --git a/modules/nf-core/arriba/download/tests/main.nf.test.snap b/modules/nf-core/arriba/download/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "download": {
+    "test-arriba-download": {
         "content": [
             {
                 "0": [
@@ -35,9 +35,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-08T11:12:17.010496"
+        "timestamp": "2024-12-16T01:46:32.110653034"
     }
 }
diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml
@@ -103,7 +103,7 @@ output:
       - ${prefix}.hypotheticals.tsv:
           type: file
           description: additional information on hypothetical protein CDS as simple human
-            readble tab separated values
+            readable tab separated values
           pattern: "*.hypotheticals.tsv"
   - hypotheticals_faa:
       - meta:
@@ -123,7 +123,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${prefix}.tsv:
           type: file
-          description: annotations as simple human readble tab separated values
+          description: annotations as simple human readable tab separated values
           pattern: "*.tsv"
   - txt:
       - meta:

diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf
@@ -26,7 +26,7 @@ process BBMAP_ALIGN {
     input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
 
     // Set the db variable to reflect the three possible types of reference input: 1) directory
-    // named 'ref', 2) directory named something else (containg a 'ref' subdir) or 3) a sequence
+    // named 'ref', 2) directory named something else (containing a 'ref' subdir) or 3) a sequence
     // file in fasta format
     if ( ref.isDirectory() ) {
         if ( ref ==~ /(.\/)?ref\/?/ ) {

diff --git a/modules/nf-core/bbmap/align/meta.yml b/modules/nf-core/bbmap/align/meta.yml
@@ -31,7 +31,7 @@ input:
         description: |
           Either "ref" a directory containing an index, the name of another directory
           with a "ref" subdirectory containing an index or the name of a fasta formatted
-          nucleotide file containg the reference to map to.
+          nucleotide file containing the reference to map to.
 output:
   - bam:
       - meta:

diff --git a/modules/nf-core/bcftools/convert/meta.yml b/modules/nf-core/bcftools/convert/meta.yml
@@ -28,7 +28,7 @@ input:
     - input:
         type: file
         description: |
-          The input format. Each format needs a seperate parameter to be specified in the `args`:
+          The input format. Each format needs a separate parameter to be specified in the `args`:
           - GEN/SAMPLE file: `--gensample2vcf`
           - gVCF file: `--gvcf2vcf`
           - HAP/SAMPLE file: `--hapsample2vcf`

diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml
@@ -24,7 +24,7 @@ input:
     - vcf:
         type: file
         description: |
-          The vcf file to be qeuried.
+          The vcf file to be queried.
         pattern: "*.{vcf.gz, vcf}"
     - tbi:
         type: file

diff --git a/modules/nf-core/bowtie/build/meta.yml b/modules/nf-core/bowtie/build/meta.yml
@@ -29,7 +29,7 @@ output:
       - meta:
           type: map
           description: |
-            Groovy Map containing nformation about the genome fasta
+            Groovy Map containing information about the genome fasta
             e.g. [ id:'test' ]
       - bowtie:
           type: file

diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
@@ -104,11 +104,11 @@ output:
   - log:
       - meta:
           type: file
-          description: Aligment log
+          description: Alignment log
           pattern: "*.log"
       - "*.log":
           type: file
-          description: Aligment log
+          description: Alignment log
           pattern: "*.log"
   - fastq:
       - meta:

diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test
@@ -1,5 +1,3 @@
-// NOTE The version snaps may not be consistant
-// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035
 nextflow_process {
 
     name "Test Process CAT_FASTQ"

diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py
@@ -21,7 +21,7 @@ def chunk_iter(seq, size):
 
 # get fastqs, ordered by path. Files are staged into
 #   - "fastq_001/{original_name.fastq.gz}"
-#   - "fastq_002/{oritinal_name.fastq.gz}"
+#   - "fastq_002/{original_name.fastq.gz}"
 #   - ...
 # Since we require fastq files in the input channel to be ordered such that a R1/R2 pair
 # of files follows each other, ordering will get us a sequence of [R1, R2, R1, R2, ...]

diff --git a/modules/nf-core/cellsnp/modea/meta.yml b/modules/nf-core/cellsnp/modea/meta.yml
@@ -50,7 +50,7 @@ output:
             e.g. `[ id:'sample1', single_end:false ]`
       - "*.base.vcf.gz":
           type: file
-          description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation
+          description: A VCF file listing genotyped SNPs and aggregated AD & DP information
             (without GT).
           pattern: "*.base.vcf.gz"
   - cell:
@@ -61,7 +61,7 @@ output:
             e.g. `[ id:'sample1', single_end:false ]`
       - "*.cells.vcf.gz":
           type: file
-          description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation
+          description: A VCF file listing genotyped SNPs and aggregated AD & DP information
             & genotype (GT) information for each cell or sample.
           pattern: "*.cells.vcf.gz"
   - sample:

diff --git a/modules/nf-core/clippy/main.nf b/modules/nf-core/clippy/main.nf
@@ -37,4 +37,18 @@ process CLIPPY {
         clippy: \$(clippy -v)
     END_VERSIONS
     """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_Peaks.bed
+    touch ${prefix}_Summits.bed
+    touch ${prefix}_intergenic_regions.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clippy: \$(clippy -v)
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/clippy/tests/main.nf.test b/modules/nf-core/clippy/tests/main.nf.test
@@ -0,0 +1,90 @@
+nextflow_process {
+
+    name "Test Process CLIPPY"
+    script "../main.nf"
+    process "CLIPPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "clippy"
+
+    test("non-intergenic") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args = '-inter 3'
+            }
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/crosslinks/clippy.bed", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("intergenic") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/crosslinks/clippy.bed", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("non-intergenic - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    []
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}