nf-core · sateeshperi · Apr 28, 2023 · May 2, 2023 · JoseEspinosa · May 2, 2023
diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/peng-lab/BaSiCPy"
       documentation: "https://basicpy.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/peng-lab/BaSiCPy"
-      doi: "doi: 10.1038/ncomms14836."
+      doi: 10.1038/ncomms14836
       licence: "MIT License"
 
 input:

diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
@@ -1,6 +1,7 @@
 name: cat_fastq
 description: Concatenates fastq files
 keywords:
+  - cat
   - fastq
   - concatenate
 tools:
@@ -16,7 +17,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - reads:
-      type: list
+      type: file
       description: |
         List of input FastQ files to be concatenated.
 output:

diff --git a/modules/nf-core/cellpose/meta.yml b/modules/nf-core/cellpose/meta.yml
@@ -2,13 +2,15 @@ name: "cellpose"
 description: cellpose segments cells in images
 keywords:
   - segmentation
+  - image
+  - cellpose
 tools:
   - "cellpose":
       description: "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu"
       homepage: "https://github.com/MouseLand/cellpose"
       documentation: "https://cellpose.readthedocs.io/en/latest/command.html"
       tool_dev_url: "https://github.com/MouseLand/cellpose"
-      doi: "https://doi.org/10.1038/s41592-022-01663-4"
+      doi: 10.1038/s41592-022-01663-4
       licence: "BSD 3-Clause"
 
 input:
@@ -18,7 +20,7 @@ input:
         Groovy Map containing sample information
         (sample id)
   - image:
-      type: image stack
+      type: file
       description: tif file for ready for segmentation
       pattern: "*.{tif,tiff}"
   - model:
@@ -36,7 +38,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - mask:
-      type: tif_file
+      type: file
       description: labelled mask output from cellpose in tif format
       pattern: "*.{tif, tiff}"
 

diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://mcmicro.org/parameters/core.html#coreograph"
       documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html"
       tool_dev_url: "https://github.com/HMS-IDAC/UNetCoreograph"
-      doi: "https://doi.org/10.1038/s41592-021-01308-y"
+      doi: 10.1038/s41592-021-01308-y
       licence: "MIT License"
 
 input:
@@ -38,7 +38,7 @@ output:
       pattern: "*.{tif}"
 
   - masks:
-      type: files
+      type: file
       description: Binary masks for the Complete/Incomplete tissue cores
       pattern: "./masks/*.{tif}"
 

diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml
@@ -3,6 +3,7 @@ description: Convert a TSV or CSV with features by row and observations by colum
 keywords:
   - gsea
   - gct
+  - tabular
 tools:
   - tabulartogseagct:
       description: "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA"

diff --git a/modules/nf-core/deepcell/mesmer/meta.yml b/modules/nf-core/deepcell/mesmer/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/vanvalenlab/deepcell-tf"
       documentation: "https://github.com/vanvalenlab/intro-to-deepcell/tree/master/pretrained_models"
       tool_dev_url: "https://githu/b.com/vanvalenlab/deepcell-tf"
-      doi: "https://doi.org/10.1038/s41587-021-01094-0"
+      doi: 10.1038/s41587-021-01094-0
       licence: "APACHE2"
 
 input:

diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml
@@ -3,6 +3,7 @@ description: DeepVariant is an analysis pipeline that uses a deep neural network
 keywords:
   - variant calling
   - machine learning
+  - neural network
 tools:
   - deepvariant:
       description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

diff --git a/modules/nf-core/eido/convert/meta.yml b/modules/nf-core/eido/convert/meta.yml
@@ -20,7 +20,7 @@ input:
       description: Nextflow samplesheet or PEP project
       pattern: "*.{yaml,yml,csv}"
   - format:
-      type: value
+      type: string
       description: Extension of an output file
   - pep_input_base_dir:
       type: file

diff --git a/modules/nf-core/fqtk/meta.yml b/modules/nf-core/fqtk/meta.yml
@@ -3,12 +3,12 @@ description: Demultiplex fastq files
 keywords:
   - demultiplex
   - fastq
+  - rust
 tools:
   - "fqtk":
       description: "A toolkit for working with FASTQ files, written in Rust."
       homepage: "https://github.com/fulcrumgenomics/fqtk"
       documentation: "https://github.com/fulcrumgenomics/fqtk"
-      tool_dev_url: "None"
       licence: "['MIT']"
 
 input:
@@ -22,7 +22,7 @@ input:
       description: Tsv file, with two columns sample_id and barcode
       pattern: "*.{tsv}"
   - fastq_readstructure_pairs:
-      type: list
+      type: map
       description: List of lists i.e. [[<fastq file name>, <read structure>, <absolute path to fastq directory>],...]
 
 output:

diff --git a/modules/nf-core/gatk4/applybqsrspark/meta.yml b/modules/nf-core/gatk4/applybqsrspark/meta.yml
@@ -3,6 +3,7 @@ description: Apply base quality score recalibration (BQSR) to a bam file
 keywords:
   - bqsr
   - bam
+  - gatk
 tools:
   - gatk4:
       description: |

diff --git a/modules/nf-core/gatk4/baserecalibratorspark/meta.yml b/modules/nf-core/gatk4/baserecalibratorspark/meta.yml
@@ -2,6 +2,8 @@ name: gatk4_baserecalibrator_spark
 description: Generate recalibration table for Base Quality Score Recalibration (BQSR)
 keywords:
   - sort
+  - bqsr
+  - gatk
 tools:
   - gatk4:
       description: |

diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml
@@ -23,15 +23,15 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - counts:
-      type: file(s)
+      type: file
       description: One or more count TSV files created with gatk/collectreadcounts
       pattern: "*.tsv"
   - bed:
       type: file
       description: Optional - A bed file containing the intervals to include in the process
       pattern: "*.bed"
   - exclude_beds:
-      type: file(s)
+      type: file
       description: Optional - One or more bed files containing intervals to exclude from the process
       pattern: "*.bed"
   - contig_ploidy_table:

diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml
@@ -3,6 +3,7 @@ description: Calls copy-number variants in germline samples given their counts a
 keywords:
   - gatk
   - gatk4_germlinecnvcaller
+  - germline contig ploidy
 tools:
   - "gatk4":
       description:
@@ -21,7 +22,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - tsv:
-      type: file(s)
+      type: file
       description: One or more count TSV files created with gatk/collectreadcounts
       pattern: "*.tsv"
   - intervals:

diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml
@@ -4,9 +4,10 @@ description: |
 keywords:
   - GNU
   - sort
+  - merge compare
 tools:
   - sort:
-      description: "Writes a sorted consatenation of file/s"
+      description: "Writes a sorted concatenation of file/s"
       homepage: "https://github.com/vgl-hub/gfastats"
       documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html"
       licence: ["GPL"]

diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
@@ -3,6 +3,7 @@ description: Compresses and decompresses files.
 keywords:
   - gunzip
   - compression
+  - decompression
 tools:
   - gunzip:
       description: |

diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml
@@ -4,13 +4,13 @@ description: Ilastik is a tool that utilizes machine learning algorithms to clas
 keywords:
   - multicut
   - segmentation
+  - pixel classification
 tools:
   - "ilastik":
       description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis."
       homepage: "https://www.ilastik.org/"
       documentation: "https://www.ilastik.org/documentation/"
       tool_dev_url: "https://github.com/ilastik/ilastik"
-      doi: ""
       licence: "GPL3"
 
 input:

diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml
@@ -11,7 +11,6 @@ tools:
       homepage: "https://www.ilastik.org/"
       documentation: "https://www.ilastik.org/documentation/"
       tool_dev_url: "https://github.com/ilastik/ilastik"
-      doi: ""
       licence: "GPL3"
 
 input:

diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml
@@ -28,12 +28,12 @@ input:
       type: directory
       description: Kraken2 database
   - save_output_fastqs:
-      type: boolean
+      type: string
       description: |
         If true, optional commands are added to save classified and unclassified reads
         as fastq files
   - save_reads_assignment:
-      type: boolean
+      type: string
       description: |
         If true, an optional command is added to save a file reporting the taxonomic
         classification of each input read

diff --git a/modules/nf-core/mcquant/meta.yml b/modules/nf-core/mcquant/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/labsyspharm/quantification"
       documentation: "https://github.com/labsyspharm/quantification/blob/master/README.md"
       tool_dev_url: "https://github.com/labsyspharm/quantification"
-      doi: "https://doi.org/10.1038/s41592-021-01308-y"
+      doi: 10.1038/s41592-021-01308-y
       licence: ""
 
 input:

diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml
@@ -2,6 +2,8 @@ name: "md5sum"
 description: Create an MD5 (128-bit) checksum
 keywords:
   - checksum
+  - MD5
+  - 128 bit
 tools:
   - "md5sum":
       description: Create an MD5 (128-bit) checksum

diff --git a/modules/nf-core/scimap/mcmicro/meta.yml b/modules/nf-core/scimap/mcmicro/meta.yml
@@ -2,13 +2,14 @@ name: "scimap_mcmicro"
 description: SCIMAP is a suite of tools that enables spatial single-cell analyses
 keywords:
   - sort
+  - spatial
+  - single cell
 tools:
   - "scimap":
       description: "Scimap is a scalable toolkit for analyzing spatial molecular data."
       homepage: "https://scimap.xyz/"
       documentation: "https://scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap/"
       tool_dev_url: "https://github.com/labsyspharm/scimap"
-      doi: ""
       licence: "MIT License"
 
 input:

diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml
@@ -52,6 +52,7 @@ output:
       description: BAM file.
       pattern: "*.bam"
   - bai:
+      type: file
       description: BAI file
       pattern: "*.bai"
   - versions:

diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml
@@ -25,6 +25,7 @@ input:
       description: BAM file.
       pattern: "*.bam"
   - bai:
+      type: file
       description: BAI file
       pattern: "*.bai"
   - fasta:
@@ -54,6 +55,7 @@ output:
       description: BAM file.
       pattern: "*.bam"
   - bai:
+      type: file
       description: BAI file
       pattern: "*.bai"
   - score:

diff --git a/modules/nf-core/sgdemux/meta.yml b/modules/nf-core/sgdemux/meta.yml
@@ -3,6 +3,7 @@ description: Demultiplex bgzip'd fastq files
 keywords:
   - demultiplex
   - fastq
+  - bgzip
 tools:
   - "sgdemux":
       description: "Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments."

diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml
@@ -3,6 +3,7 @@ description: Print SHA256 (256-bit) checksums.
 keywords:
   - checksum
   - sha256
+  - 256 bit
 tools:
   - "md5sum":
       description: Create an SHA256 (256-bit) checksum.

diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml
@@ -2,6 +2,8 @@ name: SNPEFF_SNPEFF
 description: Genetic variant annotation and functional effect prediction toolbox
 keywords:
   - annotation
+  - variant
+  - effect prediction
 tools:
   - snpeff:
       description: |
@@ -21,7 +23,7 @@ input:
       description: |
         vcf to annotate
   - db:
-      type: value
+      type: string
       description: |
         which db to annotate with
   - cache:

diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
@@ -3,6 +3,7 @@ description: Extract files.
 keywords:
   - untar
   - uncompress
+  - extract
 tools:
   - untar:
       description: |

diff --git a/modules/nf-core/untarfiles/meta.yml b/modules/nf-core/untarfiles/meta.yml
@@ -3,6 +3,7 @@ description: Extract files.
 keywords:
   - untar
   - uncompress
+  - files
 tools:
   - untar:
       description: |
@@ -26,7 +27,7 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - files:
-      type: list
+      type: string
       description: A list containing references to individual archive files
       pattern: "*/**"
   - versions:
-Original file line number
+Diff line change
@@ Expand Up @@
     keywords:
       - gsea
       - gct
+      - tabular
     tools:
       - tabulartogseagct:
           description: "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA"
@@ Expand Down @@