get test working

NBISweden · Jun 12, 2024 · bf0eacd · bf0eacd
1 parent 090c55d
commit bf0eacd
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Showing 4 changed files with 95 additions and 16 deletions.
diff --git a/config/test.config b/config/test.config
@@ -1,36 +1,36 @@
 if ( params.subworkflow == 'abinitio_training' ) {
     params {
         maker_evidence_gff = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff'
-        genome = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
-        species_label = 'test_species'  // e.g. 'asecodes_parviclava'
-        flank_region_size = 500
-        aed_value = [ 0.3, 0.2 ]
-        locus_distance = [ 500 ]
+        genome             = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
+        species_label      = 'test_species'  // e.g. 'asecodes_parviclava'
+        flank_region_size  = 500
+        aed_value          = [ 0.3, 0.2 ]
+        locus_distance     = [ 500 ]
     }
     process {
         // Trick: Fully qualified process name has higher priority than simple name
         // Otherwise settings are overridden by those in modules.config loaded after this
         withName: 'ABINITIO_TRAINING:GBK2AUGUSTUS' {
-            ext.args   = '10'
+            ext.args       = '10'
         }
     }
 }
 if ( params.subworkflow == 'annotation_preprocessing' ) {
     params {
-        genome = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
+        genome             = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
     }
 }
 if ( params.subworkflow == 'functional_annotation' ) {
     params {
-        genome = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
-        gff_annotation = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff'
+        genome             = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
+        gff_annotation     = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff'
         // blast_db_fasta = 'https://www.uniprot.org/uniprot/%3Fquery%3Dorganism%3A4932%26format%3Dfasta'
-        blast_db_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/database/yeast_UPS.fasta'
+        blast_db_fasta     = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/database/yeast_UPS.fasta'
     }
     process {
         withName: 'FUNCTIONAL_ANNOTATION:INTERPROSCAN' {
-            cpus = 2
-            ext.args = [
+            cpus           = 2
+            ext.args       = [
                 // '--iprlookup',
                 // '--goterms', 
                 // '-pa', 
@@ -41,9 +41,16 @@ if ( params.subworkflow == 'functional_annotation' ) {
 }
 if ( params.subworkflow == 'transcript_assembly' ) {
     params {
-        reads = 'https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238351_subsamp.fastq.gz'
-        genome = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
-        single_end = true
+        reads              = 'https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238351_subsamp.fastq.gz'
+        genome             = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
+        single_end         = true
+    }
+}
+
+if ( params.subworkflow == 'format_validation' ) {
+    params {
+        genome             = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
+        gff_annotation     = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff'
     }
 }
 

diff --git a/main.nf b/main.nf
@@ -18,7 +18,7 @@ workflow {
 
     '''
 
-    def valid_subworkflows = [ 'abinitio_training', 'annotation_preprocessing', 'functional_annotation', 'transcript_assembly' ]
+    def valid_subworkflows = [ 'abinitio_training', 'annotation_preprocessing', 'functional_annotation', 'transcript_assembly', 'format_validation' ]
     if( ! params.subworkflow in valid_subworkflows ){
         error """
         The parameter 'subworkflow' (value: ${params.subworkflow}) is not a valid subworkflow.

diff --git a/modules/local/embl/apivalidator.nf b/modules/local/embl/apivalidator.nf
@@ -0,0 +1,55 @@
+process EMBL_APIVALIDATOR {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::embl-api-validator:1.1.180"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/embl-api-validator:1.1.180--py36_0':
+        'biocontainers/embl-api-validator:1.1.180--py36_0' }"
+
+    input:
+    tuple val(meta), path(file), val(extension)
+
+    output:
+    tuple val(meta), env(status)                  , emit: status
+    tuple val(meta), path("*.gff3")               , emit: gff3         , optional: true
+    tuple val(meta), path("diagnose", type: 'dir'), emit: diagnosis    , optional: true
+    tuple val(meta), path("*_good.txt")           , emit: filtered_good, optional: true
+    tuple val(meta), path("*_bad.txt")            , emit: filtered_bad , optional: true
+    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}"
+    """
+    status=embl-api-validator \\
+        -f $extension \\
+        $args \\
+        -p ${prefix} \\
+        $file \\
+        || echo "\$?"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        embl-api-validator: \$(embl-api-validator -version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def mkdir_diagnose = args.contains('-fix_diagnose')? 'mkdir diagnose' : ''
+    """
+    touch ${prefix}.gff3
+    $mkdir_diagnose
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        embl-api-validator: \$(embl-api-validator -version)
+    END_VERSIONS
+    """
+}
diff --git a/subworkflows/format_validation/main.nf b/subworkflows/format_validation/main.nf
@@ -0,0 +1,17 @@
+include { EMBL_APIVALIDATOR } from "$projectDir/modules/local/embl/apivalidator"
+
+workflow FORMAT_VALIDATION {
+
+    main:
+    log.info """
+        Functional annotation workflow
+        ===================================================
+    """
+    Channel.fromPath( params.gff_annotation, checkIfExists: true )
+        .map { gff -> [ [ id: gff.baseName ], gff ] }
+        .set { gff_file }
+    Channel.fromPath( params.genome, checkIfExists: true )
+        .set { genome }
+
+    EMBL_APIVALIDATOR ( gff_file.map { meta, gff -> [ meta, gff, gff.getExtension() ] } )
+}