Add eido/convert module (#2051)

* Add eido/convert module

* Run prettier

* Update modules/eido/convert/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/eido/convert/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update extension format

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/eido/convert/main.nf

@@ -0,0 +1,37 @@
+process EIDO_CONVERT {
+    tag '$samplesheet'
+    label 'process_single'
+
+    conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
+        'biocontainers/eido:0.1.9_cv1' }"
+
+    input:
+    path samplesheet
+    val format
+
+    output:
+    path "versions.yml"           , emit: versions
+    path "${prefix}.${format}"    , emit: samplesheet_converted
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "samplesheet_converted"
+    """
+    eido \\
+        convert \\
+        -f $format \\
+        $samplesheet \\
+        $args \\
+        -p samples=${prefix}.${format}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
+    END_VERSIONS
+    """
+}

modules/eido/convert/meta.yml

@@ -0,0 +1,36 @@
+name: "eido_convert"
+description: Convert any PEP project or Nextflow samplesheet to any format
+keywords:
+  - eido
+  - convert
+  - PEP
+  - format
+  - samplesheet
+tools:
+  - "eido":
+      description: "Convert any PEP project or Nextflow samplesheet to any format"
+      homepage: "http://eido.databio.org/en/latest/"
+      documentation: "http://eido.databio.org/en/latest/"
+      doi: "10.1093/gigascience/giab077"
+      licence: "BSD-2-Clause"
+
+input:
+  - samplesheet:
+      type: file
+      description: Nextflow samplesheet or PEP project
+      pattern: "*.{yaml,yml,csv}"
+  - format:
+      type: value
+      description: Extension of an output file
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - samplesheet_converted:
+      type: file
+      description: PEP project or samplesheet converted to csv file
+
+authors:
+  - "@rafalstepien"

tests/config/pytest_modules.yml

@@ -687,14 +687,18 @@ ectyper:
   - modules/ectyper/**
   - tests/modules/ectyper/**
 
-elprep/filter:
+eido/convert:
-  - modules/elprep/filter/**
+  - modules/eido/convert/**
-  - tests/modules/elprep/filter/**
+  - tests/modules/eido/convert/**
 
 eido/validate:
   - modules/eido/validate/**
   - tests/modules/eido/validate/**
 
+elprep/filter:
+  - modules/elprep/filter/**
+  - tests/modules/elprep/filter/**
+
 elprep/merge:
   - modules/elprep/merge/**
   - tests/modules/elprep/merge/**

tests/modules/eido/convert/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EIDO_CONVERT } from '../../../../modules/eido/convert/main.nf'
+
+workflow test_eido_convert_nextflow_samplesheet {
+
+    nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
+    format = "csv"
+
+    EIDO_CONVERT ( nextflow_samplesheet, format )
+}
+
+
+workflow test_eido_convert_pep_project {
+
+    pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
+    format = "csv"
+
+    EIDO_CONVERT ( pep_project, format )
+}

tests/modules/eido/convert/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: 'EIDO_CONVERT' {
+        ext.args = '--st-index sample'
+    }
+}

tests/modules/eido/convert/test.yml

@@ -0,0 +1,17 @@
+- name: eido convert test_eido_convert_nextflow_samplesheet
+  command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
+  tags:
+    - eido
+    - eido/convert
+  files:
+    - path: output/eido/samplesheet_converted.csv
+      md5sum: 7aa4da4944650b9c7c451c5dfbeae663
+
+- name: eido convert test_eido_convert_pep_project
+  command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
+  tags:
+    - eido
+    - eido/convert
+  files:
+    - path: output/eido/samplesheet_converted.csv
+      md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda