Fix minor typos (nf-core#7177)

* Fix minor typos * Uppercase f in MAF * Update modules/nf-core/popscle/freemuxlet/meta.yml Co-authored-by: Edmund Miller <[email protected]> * Update snapshots * Remove parabricks pytest * Reset iqtree tool typo * Update modules/nf-core/cat/fastq/tests/main.nf.test * Remove ivar/consensus from pytest * Move gatk4/asereadcounter tests into subfolder * Remove empty environment and unused variables from coreograph --------- Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>
fellen31 · Jan 10, 2025 · 1254968 · 1254968
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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/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/clonalframeml/meta.yml b/modules/nf-core/clonalframeml/meta.yml
@@ -21,11 +21,11 @@ input:
           e.g. [ id:'test', single_end:false ]
     - newick:
         type: file
-        description: A Newick formated tree based on multiple sequence alignment
+        description: A Newick formatted tree based on multiple sequence alignment
         pattern: "*.{newick,treefile,dnd}"
     - msa:
         type: file
-        description: A multiple seqeunce alignmnet in FASTA format
+        description: A multiple sequence alignment in FASTA format
         pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
 output:
   - emsim:

diff --git a/modules/nf-core/concoct/concoct/meta.yml b/modules/nf-core/concoct/concoct/meta.yml
@@ -94,7 +94,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*_PCA_transformed_data_gt1000.csv":
           type: file
-          description: Transformed PCA compontent values
+          description: Transformed PCA component values
           pattern: "*_PCA_transformed_data_gt1000.csv"
   - versions:
       - versions.yml:

diff --git a/modules/nf-core/concoct/mergecutupclustering/meta.yml b/modules/nf-core/concoct/mergecutupclustering/meta.yml
@@ -37,7 +37,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.csv":
           type: file
-          description: Cluster assignments per contig part with concensus cluster
+          description: Cluster assignments per contig part with consensus cluster
           pattern: "*.csv"
   - versions:
       - versions.yml:

diff --git a/modules/nf-core/cooler/balance/meta.yml b/modules/nf-core/cooler/balance/meta.yml
@@ -36,7 +36,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${prefix}.${extension}:
           type: file
-          description: Output COOL file balancing weigths
+          description: Output COOL file balancing weights
           pattern: "*.cool"
   - versions:
       - versions.yml:

diff --git a/modules/nf-core/coreograph/environment.yml b/modules/nf-core/coreograph/environment.yml
diff --git a/modules/nf-core/coreograph/main.nf b/modules/nf-core/coreograph/main.nf
@@ -8,9 +8,9 @@ process COREOGRAPH {
     tuple val(meta), path(image)
 
     output:
-    tuple val(meta), path("*[0-9]*.tif"), emit: cores
-    tuple val(meta), path("./masks/"), emit: masks
-    tuple val(meta), path("TMA_MAP.tif"), emit: tma_map
+    tuple val(meta), path("*[0-9]*.tif")     , emit: cores
+    tuple val(meta), path("./masks/")        , emit: masks
+    tuple val(meta), path("TMA_MAP.tif")     , emit: tma_map
     tuple val(meta), path("centroidsY-X.txt"), emit: centroids
 
     path "versions.yml" , emit: versions
@@ -20,8 +20,7 @@ process COREOGRAPH {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.2.9'
+    def VERSION = '2.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
     python /app/UNetCoreograph.py \\
@@ -37,7 +36,7 @@ process COREOGRAPH {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch TMA_MAP.tif
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml
@@ -10,7 +10,7 @@ keywords:
   - Cores
 tools:
   - "coreograph":
-      description: "A TMA dearray porgram that uses UNet, a deep learning model, to
+      description: "A TMA dearray program that uses UNet, a deep learning model, to
         identify complete/incomplete tissue cores on a tissue microarray."
       homepage: "https://mcmicro.org/parameters/core.html#coreograph"
       documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html"

diff --git a/modules/nf-core/crumble/meta.yml b/modules/nf-core/crumble/meta.yml
@@ -29,7 +29,7 @@ input:
         description: BED file defining regions to keep quality
   - - bedout:
         type: boolean
-        description: set to true to ouput suspicious regions to a BED file
+        description: set to true to output suspicious regions to a BED file
 output:
   - bam:
       - meta:

diff --git a/modules/nf-core/custom/matrixfilter/templates/matrixfilter.R b/modules/nf-core/custom/matrixfilter/templates/matrixfilter.R
@@ -143,7 +143,7 @@ if (opt\$sample_file != ''){
 
     # If we're not using a sample sheet to select columns, then at least make
     # sure the ones we have are numeric (some upstream things like the RNA-seq
-    # workflow have annotation colummns as well)
+    # workflow have annotation columns as well)
 
     numeric_columns <- unlist(lapply(1:ncol(abundance_matrix), function(x) is.numeric(abundance_matrix[,x])))
     abundance_matrix <- abundance_matrix[,numeric_columns]

diff --git a/modules/nf-core/deeptools/alignmentsieve/meta.yml b/modules/nf-core/deeptools/alignmentsieve/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - ATACshift
 tools:
   - deeptools:
-      description: A set of user-friendly tools for normalization and visualzation of
+      description: A set of user-friendly tools for normalization and visualization of
         deep-sequencing data
       homepage: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html
       documentation: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html

diff --git a/modules/nf-core/deeptools/bamcoverage/meta.yml b/modules/nf-core/deeptools/bamcoverage/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - track
 tools:
   - deeptools:
-      description: A set of user-friendly tools for normalization and visualzation of
+      description: A set of user-friendly tools for normalization and visualization of
         deep-sequencing data
       homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
       documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html

diff --git a/modules/nf-core/duphold/main.nf b/modules/nf-core/duphold/main.nf
@@ -8,7 +8,7 @@ process DUPHOLD {
         'biocontainers/duphold:0.2.1--h516909a_1' }"
 
     input:
-    tuple val(meta), path(alignment_file), path(alignement_index), path(sv_variants), path(snp_variants), path(snp_variants_index)
+    tuple val(meta), path(alignment_file), path(alignment_index), path(sv_variants), path(snp_variants), path(snp_variants_index)
     path(fasta)
     path(fasta_fai)
 

diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml
@@ -29,7 +29,7 @@ input:
     - alignment_file:
         type: file
         description: file containing alignments
-    - alignement_index:
+    - alignment_index:
         type: file
         description: index of alignment file
     - sv_variants:

diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml
@@ -94,7 +94,7 @@ input:
           given file in IGV format.
   - - get_assembly_regions:
         type: boolean
-        description: Get the assembly regions calculated by haplotypecaller to the speficied
+        description: Get the assembly regions calculated by haplotypecaller to the specified
           file in IGV format.
 output:
   - bam:

diff --git a/modules/nf-core/fcsgx/fetchdb/tests/main.nf.test b/modules/nf-core/fcsgx/fetchdb/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                // Some output files are too large to calcualte MD5sums, so we just list the files in the output directory.
+                // Some output files are too large to calculate MD5sums, so we just list the files in the output directory.
                 { assert snapshot(
                         file(process.out.database.get(0)).list().sort(),
                         process.out.versions

diff --git a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml
@@ -34,7 +34,7 @@ input:
         type: string
         enum: ["Identity", "Edit", "Adjacency", "Paired"]
         description: |
-          Reguired argument: defines the UMI assignment strategy.
+          Required argument: defines the UMI assignment strategy.
           Must be chosen among: Identity, Edit, Adjacency, Paired.
 output:
   - bam:

diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml
@@ -79,12 +79,12 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.intervals":
           type: file
-          description: File containg intervals that represent sites of extant and potential
+          description: File containing intervals that represent sites of extant and potential
             indels.
           pattern: "*.intervals"
       - s:
           type: file
-          description: File containg intervals that represent sites of extant and potential
+          description: File containing intervals that represent sites of extant and potential
             indels.
           pattern: "*.intervals"
   - versions:

diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml
@@ -1,5 +1,5 @@
 name: "gatk4_asereadcounter"
-description: Calculates the allele-specific read counts for alle-specific expression
+description: Calculates the allele-specific read counts for allele-specific expression
   analysis of RNAseq data
 keywords:
   - allele-specific

diff --git a/...nf-core/gatk4/asereadcounter/main.nf.test → ...e/gatk4/asereadcounter/tests/main.nf.test b/...nf-core/gatk4/asereadcounter/main.nf.test → ...e/gatk4/asereadcounter/tests/main.nf.test
diff --git a/...re/gatk4/asereadcounter/main.nf.test.snap → ...k4/asereadcounter/tests/main.nf.test.snap b/...re/gatk4/asereadcounter/main.nf.test.snap → ...k4/asereadcounter/tests/main.nf.test.snap