Merge pull request #67 from EBI-Metagenomics/proovframe-fix

Proovframe fix

modules/ebi-metagenomics/proovframe/fix/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::proovframe=0.9.7"

modules/ebi-metagenomics/proovframe/fix/main.nf

@@ -0,0 +1,49 @@
+process PROOVFRAME_FIX {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/proovframe:0.9.7--hdfd78af_1':
+        'biocontainers/proovframe:0.9.7--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(fa)
+    tuple val(meta2), path(tsv)
+
+    output:
+    tuple val(meta), path("*.fa"), emit: out_fa
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    proovframe   \\
+        fix \\
+        ${args} \\
+        -o ${prefix}.fa  \\
+        ${fa} \\
+        ${tsv}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        proovframe: 0.9.7
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        proovframe: 0.9.7
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/proovframe/fix/meta.yml

@@ -0,0 +1,61 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "proovframe_fix"
+description: frame-shift correction for long read (meta)genomics - fix frameshifts
+  in reads
+keywords:
+  - frame-shift correction
+  - long-read sequencing
+  - sequence analysis
+tools:
+  - "proovframe":
+      description: "frame-shift correction for long read (meta)genomics"
+      homepage: "https://github.com/thackl/proovframe"
+      documentation: "https://github.com/thackl/proovframe"
+      tool_dev_url: "https://github.com/thackl/proovframe"
+      doi: "10.1101/2021.08.23.457338"
+      licence: ["MIT"]
+      identifier: biotools:proovframe
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fa:
+        type: file
+        description: "A FASTA file containing a database of guide protein sequences"
+        pattern: "*.{faa,fasta,fa}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - tsv:
+        type: file
+        description: "Output TSV file with the frameshift-aware protein to read alignments\
+          \ from proovframe/map"
+        pattern: "*.{tsv}"
+
+output:
+  - out_fa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.fa":
+          type: file
+          description: "Result FASTA with fixed frameshift reads"
+          pattern: "*.{fa}"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@mcarbajo"
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"