Update nf

.github/workflows/linting.yml

@@ -36,7 +36,7 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: "3.6"
+          python-version: "3.11.3"
           architecture: "x64"
 
       - name: Install dependencies

.nf-core.yml

@@ -29,10 +29,10 @@ lint:
     # We don't use AWS
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
-  nextflow_config: false
+  nextflow_config:
   # Currently not supported, but hopefully soon!
   # See https://github.com/nf-core/tools/issues/1031
-  # - mainfest.name
+    - mainfest.name
   # - manifest.homePage
   files_unchanged:
     - .markdownlint.yml
@@ -55,3 +55,4 @@ lint:
     # Can't find minimum NF version and doesn't like the addition of 'dispatch'
     # to the events
   template_strings: false
+org_path: ksumngs

README.md

@@ -51,7 +51,7 @@ nextflow run ksumngs/v-met               \
 ### Example: Illumina reads with a relatively complete Kraken2 database
 
 ```bash
-nextflow run ksumngs/yavsap          \
+nextflow run ksumngs/v-met          \
   -profile singularity               \
   --platform illumina                \
   --kraken2_db /databases/kraken2/nt \
@@ -61,7 +61,7 @@ nextflow run ksumngs/yavsap          \
 ### Example: Nanopore reads with a viral-only Kraken2 database
 
 ```bash
-nextflow run ksumngs/yavsap             \
+nextflow run ksumngs/v-met             \
   -profile podman                       \
   --platform nanopore                   \
   --kraken2_db /databases/kraken2/viral \

modules.json

@@ -1,54 +1,95 @@
 {
-    "name": "v-met",
+    "name": "ksumngs/v-met",
     "homePage": "https://ksumngs.github.io/v-met",
     "repos": {
-        "ksumngs/nf-modules": {
-            "cat/fastq": {
-                "git_sha": "da5728117c6caaee428ed8729e88b93abc60c5fc"
-            },
-            "kraken2": {
-                "git_sha": "e0b2138159eab5b54a4618f320895a308fcf53fa"
-            },
-            "krakentools/extract": {
-                "git_sha": "181a04778a81494dc71b1d68b514b43cfef1512c"
-            },
-            "krakentools/kreport2krona": {
-                "git_sha": "c6c9d4fad20eb77232756fc08403fbc4e9988ce2"
-            },
-            "krona/importtext": {
-                "git_sha": "f423673c57aba461cf16bd3bc628e36e33b20029"
-            },
-            "nanofilt": {
-                "git_sha": "8e2140d607a9bbbf82ddf1604609f22e7371f9fb"
-            },
-            "nanostat": {
-                "git_sha": "89fce539f438cc7109b85fb7a5b75d5091382d54"
-            },
-            "trimmomatic": {
-                "git_sha": "78eb5cef96c8bbe59838c03c281780da50cfdef2"
+        "https://github.com/ksumngs/nf-modules": {
+            "modules": {
+                "ksumngs": {
+                    "cat/fastq": {
+                        "branch": "master",
+                        "git_sha": "f39d201931b5eecdc15d2605e3cad9751df462a9",
+                        "installed_by": ["modules"]
+                    },
+                    "kraken2": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krakentools/extract": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krakentools/kreport2krona": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/importtext": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "nanofilt": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "nanostat": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "trimmomatic": {
+                        "branch": "master",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    }
+                }
             }
         },
-        "nf-core/modules": {
-            "blast/blastn": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "custom/dumpsoftwareversions": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "fastqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "multiqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "seqkit/split2": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "seqtk/mergepe": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "blast/blastn": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqkit/split2": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqtk/mergepe": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqtk/seq": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    }
+                }
             },
-            "seqtk/seq": {
-                "git_sha": "1016c9bd1a7b23e31b8215b8c33095e733080735"
+            "subworkflows": {
+                "nf-core": {}
             }
         }
     }

modules/ksumngs/nf-modules/cat/fastq/main.nf → modules/ksumngs/cat/fastq/main.nf

@@ -57,7 +57,7 @@ process CAT_FASTQ {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            gzip: echo \$(gzip --version | head -n1 | sed 's/^gzip //')
+            gzip: \$(gzip --version | head -n1 | sed 's/^gzip //')
         END_VERSIONS
         """
     }

modules/ksumngs/nf-modules/krakentools/extract/meta.yml → modules/ksumngs/krakentools/extract/meta.yml

@@ -9,7 +9,7 @@ tools:
       description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
       homepage: https://ccb.jhu.edu/software/krakentools/
       tool_dev_url: https://github.com/jenniferlu717/KrakenTools
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:
@@ -25,8 +25,8 @@ input:
       type: file
       description: Kraken output describing the classification of each reads
   - kreport:
-        type: file
-        description: Kraken report with aggregate classification stats
+      type: file
+      description: Kraken report with aggregate classification stats
   - taxids:
       type: string
       description: Space-separated list of taxonomic ids to extract

modules/ksumngs/nf-modules/krakentools/kreport2krona/meta.yml → modules/ksumngs/krakentools/kreport2krona/meta.yml

@@ -1,32 +1,27 @@
 name: krakentools_kreport2krona
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: Takes a Kraken report file and prints out a krona-compatible TEXT file
 keywords:
-  - sort
+  - kraken
+  - krona
+  - metagenomics
+  - visualization
 tools:
   - krakentools:
-      ## TODO nf-core: Add a description and other details for the software below
       description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
-      homepage: None
-      documentation: None
-      tool_dev_url: None
-      doi: ""
-      licence: ['GPL v3']
+      homepage: https://github.com/jenniferlu717/KrakenTools
+      licence: ["GPL v3"]
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+  - kreport:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: Kraken report
+      pattern: "*.{txt,kreport}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   - meta:
       type: map
@@ -37,11 +32,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
+  - krona:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: Krona text file converted from Kraken report
+      pattern: "*.{krona}"
 
 authors:
   - "@MillironX"

modules/ksumngs/nf-modules/krona/importtext/meta.yml → modules/ksumngs/krona/importtext/meta.yml

@@ -8,7 +8,7 @@ tools:
   - krona:
       description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
       homepage: https://github.com/marbl/Krona/wiki
-      licence: ['BSD']
+      licence: ["BSD"]
 
 input:
   - krona:

modules/ksumngs/nf-modules/nanofilt/meta.yml → modules/ksumngs/nanofilt/meta.yml

@@ -8,7 +8,7 @@ tools:
       homepage: https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/
       tool_dev_url: https://github.com/wdecoster/nanofilt
       doi: "10.1093/bioinformatics/bty149"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -40,6 +40,5 @@ output:
       description: File with stats on filtered reads
       pattern: "*.{log}"
 
-
 authors:
   - "@MillironX"

modules/ksumngs/nf-modules/nanostat/meta.yml → modules/ksumngs/nanostat/meta.yml

@@ -8,7 +8,7 @@ tools:
       description: Calculate statistics for Oxford Nanopore sequencing data and alignments
       homepage: https://github.com/wdecoster/nanostat
       doi: "10.1093/bioinformatics/bty149"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -36,6 +36,5 @@ output:
       description: Read/alignment statistics report
       pattern: "*.{log}"
 
-
 authors:
   - "@MillironX"

modules/ksumngs/nf-modules/trimmomatic/meta.yml → modules/ksumngs/trimmomatic/meta.yml

@@ -8,7 +8,7 @@ tools:
       homepage: http://www.usadellab.org/cms/?page=trimmomatic
       tool_dev_url: https://github.com/usadellab/Trimmomatic
       doi: "10.1093/bioinformatics/btu170"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

modules/nf-core/modules/blast/blastn/main.nf → modules/nf-core/blast/blastn/main.nf

@@ -2,10 +2,10 @@ process BLAST_BLASTN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
+    conda "bioconda::blast=2.13.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' :
-        'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
+        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -22,7 +22,7 @@ process BLAST_BLASTN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
+    DB=`find -L ./ -name "*.ndb" | sed 's/\\.ndb\$//'`
     blastn \\
         -num_threads $task.cpus \\
         -db \$DB \\

modules/nf-core/modules/custom/dumpsoftwareversions/main.nf → modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -1,11 +1,11 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions

modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml → modules/nf-core/custom/dumpsoftwareversions/meta.yml

@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: custom_dumpsoftwareversions
 description: Custom module used to dump software versions within the nf-core pipeline template
 keywords:
   - custom
+  - dump
   - version
 tools:
   - custom: