New module suppa/psiperevents

modules/nf-core/suppa/psiperevent/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - bioconda::suppa=2.4

modules/nf-core/suppa/psiperevent/main.nf

@@ -0,0 +1,43 @@
+process SUPPA_PSIPEREVENT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d8/d887a6a05dec2a1f64fdff0eac40581f9a1ec30301b2c267bde7f564b0f14270/data' :
+        'community.wave.seqera.io/library/suppa:2.4--2612fcca3884f6bc' }"
+
+    input:
+    tuple val(meta), path(expression)
+    tuple val(meta2), path(ioe)
+    val total_filter
+
+    output:
+    tuple val(meta), path("*.psi"), emit: psi
+    tuple val("${task.process}"), val('suppa'), eval("suppa.py -v | sed '1!d;s/.* //'"), topic: versions, emit: versions_suppa
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    suppa.py \\
+        psiPerEvent \\
+        --ioe-file ${ioe} \\
+        --expression-file ${expression} \\
+        --total-filter ${total_filter} \\
+        --output-file ${prefix} \\
+        ${args}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}.psi
+    """
+}

modules/nf-core/suppa/psiperevent/meta.yml

@@ -0,0 +1,81 @@
+name: "suppa_psiperevent"
+description: "Calculate PSI values for alternative splicing events using SUPPA"
+keywords:
+  - alternative splicing
+  - suppa
+  - psi
+  - genomics
+tools:
+  - "suppa":
+      description: "Fast, accurate, and uncertainty-aware differential splicing analysis
+        across multiple conditions."
+      homepage: "https://github.com/comprna/SUPPA"
+      documentation: "https://github.com/comprna/SUPPA"
+      tool_dev_url: "https://github.com/comprna/SUPPA"
+      doi: "10.1186/s13059-018-1417-1"
+      licence:
+        - "MIT"
+      identifier: biotools:suppa
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - expression:
+        type: file
+        description: Expression matrix file in TPM units
+        pattern: "*.txt"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing genome information
+          e.g. `[ id:'genome1' ]`
+    - ioe:
+        type: file
+        description: Events file in ioe format
+        pattern: "*.ioe"
+        ontologies: []
+  - total_filter:
+      type: integer
+      description: Minimum total expression of the transcripts involved in the
+        event to be considered for PSI calculation (default = 0)
+output:
+  psi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.psi":
+          type: file
+          description: PSI values file
+          pattern: "*.psi"
+          ontologies: []
+  versions_suppa:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - suppa:
+          type: string
+          description: The name of the tool
+      - "suppa.py -v | sed '1!d;s/.* //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - suppa:
+          type: string
+          description: The name of the tool
+      - "suppa.py -v | sed '1!d;s/.* //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@lathikaa"
+  - "@piplus2"
+maintainers:
+  - "@piplus2"