🔀 Merge pull request #25 from cnr-ibba/issue-22

🚚 move nf-core modules in nf-core subfolder
cnr-ibba · Dec 18, 2023 · 7ce2c52 · 7ce2c52
2 parents f96703a + 60c857e
commit 7ce2c52
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diff --git a/.github/workflows/nf-core-linting.yml b/.github/workflows/nf-core-linting.yml
@@ -54,9 +54,8 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-        # Install a nf-core/tools custom release
       - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/bunop/tools.git@custom-modules
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
       - name: Install Nextflow
         env:

diff --git a/modules/cnr-ibba/bamaddrg/environment.yml b/modules/cnr-ibba/bamaddrg/environment.yml
@@ -0,0 +1,7 @@
+name: bamaddrg
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f
diff --git a/modules/cnr-ibba/bamaddrg/main.nf b/modules/cnr-ibba/bamaddrg/main.nf
@@ -3,10 +3,10 @@ process BAMADDRG {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1':
-        'quay.io/biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }"
+        'biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/cnr-ibba/bamaddrg/meta.yml b/modules/cnr-ibba/bamaddrg/meta.yml
@@ -2,14 +2,17 @@ name: "bamaddrg"
 description: adds read groups to input BAM files
 keywords:
   - sort
+  - add
+  - read
+  - group
+  - bam
 tools:
   - "bamaddrg":
       description: "Add read group to BAM files"
       homepage: "https://github.com/ekg/bamaddrg"
       documentation: "https://github.com/ekg/bamaddrg"
       tool_dev_url: "https://github.com/ekg/bamaddrg"
-      doi: ""
-      licence: "['MIT']"
+      licence: ["MIT"]
 
 input:
   # Only when we have meta

diff --git a/modules/cnr-ibba/bamtools/coverage/environment.yml b/modules/cnr-ibba/bamtools/coverage/environment.yml
@@ -0,0 +1,7 @@
+name: bamtools_coverage
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bamtools=2.5.2
diff --git a/modules/cnr-ibba/bamtools/coverage/main.nf b/modules/cnr-ibba/bamtools/coverage/main.nf
@@ -3,10 +3,10 @@ process BAMTOOLS_COVERAGE {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0':
-        'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hdcf5f25_2' :
+        'biocontainers/bamtools:2.5.2--hdcf5f25_2' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/cnr-ibba/bamtools/coverage/meta.yml b/modules/cnr-ibba/bamtools/coverage/meta.yml
@@ -6,13 +6,12 @@ keywords:
   - bam
   - coverage
 tools:
-  - "bamtools":
-      description: "C++ API & command-line toolkit for working with BAM data"
-      homepage: "http://github.com/pezmaster31/bamtools"
-      documentation: "https://github.com/pezmaster31/bamtools/wiki"
-      tool_dev_url: "http://github.com/pezmaster31/bamtools"
-      doi: ""
-      licence: "['MIT']"
+  - bamtools:
+      description: C++ API & command-line toolkit for working with BAM data
+      homepage: http://github.com/pezmaster31/bamtools
+      documentation: https://github.com/pezmaster31/bamtools/wiki
+      tool_dev_url: http://github.com/pezmaster31/bamtools
+      licence: ["MIT"]
 
 input:
   - meta:

diff --git a/modules/cnr-ibba/freebayes/chunk/environment.yml b/modules/cnr-ibba/freebayes/chunk/environment.yml
@@ -0,0 +1,7 @@
+name: freebayes_chunk
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::freebayes=1.3.6
diff --git a/modules/cnr-ibba/freebayes/chunk/main.nf b/modules/cnr-ibba/freebayes/chunk/main.nf
@@ -4,10 +4,10 @@ process FREEBAYES_CHUNK {
     label 'process_low'
     label 'error_retry'
 
-    conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0':
-        'quay.io/biocontainers/freebayes:1.3.6--hb089aa1_0' }"
+        'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
 
     input:
     tuple val(meta), val(region)

diff --git a/modules/cnr-ibba/freebayes/chunk/meta.yml b/modules/cnr-ibba/freebayes/chunk/meta.yml
@@ -1,36 +1,45 @@
 name: "freebayes_chunk"
-description: Run freebayes on sample
+description: Run freebayes on a sample chunk
 keywords:
   - freebayes
-  - single
+  - chunk
+  - variant caller
+  - SNP
+  - genotyping
+  - bayesian
 tools:
-  - "freebayes":
-      description: "Bayesian haplotype-based polymorphism discovery and genotyping"
-      homepage: "https://github.com/freebayes/freebayes"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
-      licence: "['MIT']"
+  - freebayes:
+      description: Bayesian haplotype-based polymorphism discovery and genotyping
+      homepage: https://github.com/freebayes/freebayes
+      documentation: https://github.com/freebayes/freebayes
+      tool_dev_url: https://github.com/freebayes/freebayes
+      doi: "10.48550/arXiv.1207.3907"
+      license: ["MIT"]
 
 input:
   - meta:
+      type: map
+      description: |
+        Groovy Map containing information on a region
+        e.g. [ id:'test', single_end:false ]
+  - sample_meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - region:
-      type: value
+      type: string
       description: A region in which genotypes will be called (chrom:start-end)
   - bam:
-      type: path
+      type: file
       description: a BAM file
       pattern: "*.{bam}"
   - bai:
       type: file
       description: Index for BAM file
       pattern: "*.{bai}"
   - bam_list:
-      type: path
+      type: file
       description: A txt file in which all bam file names are described
       pattern: "*.list.txt"
   - genome_fasta:
@@ -49,14 +58,14 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: path
+      type: file
       description: VCF compressed with bgzip
       pattern: "*.{vcf.gz}"
   - index:
-      type: path
+      type: file
       description: VCF indexed with tabix
       pattern: "*.{vcf.gz.tbi}"
-  - version:
+  - versions:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"

diff --git a/modules/cnr-ibba/freebayes/multi/environment.yml b/modules/cnr-ibba/freebayes/multi/environment.yml
@@ -0,0 +1,9 @@
+name: freebayes_multi
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::freebayes=1.3.6
+  - main::numpy
+  - main::scipy
diff --git a/modules/cnr-ibba/freebayes/multi/main.nf b/modules/cnr-ibba/freebayes/multi/main.nf
@@ -3,8 +3,8 @@ process FREEBAYES_MULTI {
     tag "freebayes.multi"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null)
-    container "bunop/freebayes:v0.1"
+    conda "${moduleDir}/environment.yml"
+    container "docker.io/bunop/freebayes:v0.1"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/cnr-ibba/freebayes/multi/meta.yml b/modules/cnr-ibba/freebayes/multi/meta.yml
@@ -3,14 +3,18 @@ description: Run freebayes on multiple BAM files
 keywords:
   - freebayes
   - multi
+  - variant caller
+  - SNP
+  - genotyping
+  - bayesian
 tools:
   - freebayes:
       description: Bayesian haplotype-based polymorphism discovery and genotyping
       homepage: https://github.com/freebayes/freebayes
-      documentation: None
-      tool_dev_url: None
-      doi: ""
-      licence: ["MIT"]
+      documentation: https://github.com/freebayes/freebayes
+      tool_dev_url: https://github.com/freebayes/freebayes
+      doi: "10.48550/arXiv.1207.3907"
+      license: ["MIT"]
 
 input:
   - meta:
@@ -19,15 +23,15 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - bam:
-      type: path
+      type: file
       description: A list of BAM files
       pattern: "*.{bam}"
   - bai:
-      type: path
+      type: file
       description: A list of BAM index files
       pattern: "*.{bai}"
   - genome_fasta:
-      type: path
+      type: file
       description: The genome fasta file (not compressed)
       pattern: "*.{fa,fasta}"
   - genome_fasta_fai:
@@ -42,14 +46,14 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: path
+      type: file
       description: |
         VCF compressed with bgzip (always all.fb.vcf.gz)
   - index:
-      type: path
+      type: file
       description: |
         VCF indexed with tabix (always all.fb.vcf.gz.tbi)
-  - version:
+  - versions:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"

diff --git a/modules/cnr-ibba/freebayes/single/environment.yml b/modules/cnr-ibba/freebayes/single/environment.yml
@@ -0,0 +1,7 @@
+name: freebayes_single
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::freebayes=1.3.6
diff --git a/modules/cnr-ibba/freebayes/single/main.nf b/modules/cnr-ibba/freebayes/single/main.nf
@@ -3,10 +3,10 @@ process FREEBAYES_SINGLE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0' :
-        'quay.io/biocontainers/freebayes:1.3.6--hb089aa1_0' }"
+        'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0':
+        'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/cnr-ibba/freebayes/single/meta.yml b/modules/cnr-ibba/freebayes/single/meta.yml
@@ -3,14 +3,18 @@ description: Run freebayes on sample
 keywords:
   - freebayes
   - single
+  - variant caller
+  - SNP
+  - genotyping
+  - bayesian
 tools:
-  - "freebayes":
-      description: "Bayesian haplotype-based polymorphism discovery and genotyping"
-      homepage: "https://github.com/freebayes/freebayes"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
-      licence: "['MIT']"
+  - freebayes:
+      description: Bayesian haplotype-based polymorphism discovery and genotyping
+      homepage: https://github.com/freebayes/freebayes
+      documentation: https://github.com/freebayes/freebayes
+      tool_dev_url: https://github.com/freebayes/freebayes
+      doi: "10.48550/arXiv.1207.3907"
+      license: ["MIT"]
 
 input:
   - meta:
@@ -19,13 +23,17 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - bam:
-      type: path
+      type: file
       description: a BAM file
       pattern: "*.{bam}"
   - bai:
       type: file
       description: Index for BAM file
       pattern: "*.{bai}"
+  - coverage:
+      type: file
+      description: Bamtools coverage output
+      pattern: "*.{txt}"
   - genome_fasta:
       type: file
       description: The genome fasta file (not compressed)
@@ -35,7 +43,7 @@ input:
       description: reference fasta file index
       pattern: "*.{fa,fasta}.fai"
   - num_regions:
-      type: optional value
+      type: integer
       description: Number of regions to split freebayes input (default $task.cpus)
 
 output:
@@ -45,14 +53,14 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: path
+      type: file
       description: VCF compressed with bgzip
       pattern: "*.{vcf.gz}"
   - index:
-      type: path
+      type: file
       description: VCF indexed with tabix
       pattern: "*.{vcf.gz.tbi}"
-  - version:
+  - versions:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"

diff --git a/modules/cnr-ibba/freebayes/splitbam/environment.yml b/modules/cnr-ibba/freebayes/splitbam/environment.yml
@@ -0,0 +1,9 @@
+name: freebayes_splitbam
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::freebayes=1.3.6
+  - main::numpy
+  - main::scipy
diff --git a/modules/cnr-ibba/freebayes/splitbam/main.nf b/modules/cnr-ibba/freebayes/splitbam/main.nf
@@ -3,8 +3,8 @@ process FREEBAYES_SPLITBAM {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null)
-    container "bunop/freebayes:v0.1"
+    conda "${moduleDir}/environment.yml"
+    container "docker.io/bunop/freebayes:v0.1"
 
     input:
     tuple val(meta), path(bam)