Update lofreq call & lofreq callparallel modules (#3812)

* Update lofreq call module & tests. Now it takes intervals input. * Update lofreq callparallel module. Now it takes intervals as input. Also updated tests. * Fix linting where entry for keywords was too short in meta.yml.
nf-core · Sep 5, 2023 · 780e332 · 780e332
1 parent 4fb6fdc
commit 780e332
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Showing 8 changed files with 69 additions and 5 deletions.
diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf
@@ -8,7 +8,7 @@ process LOFREQ_CALL {
         'biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(intervals)
     path fasta
 
     output:
@@ -21,10 +21,12 @@ process LOFREQ_CALL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def options_intervals = intervals ? "-l ${intervals}" : ""
     """
     lofreq \\
         call \\
         $args \\
+        $options_intervals \\
         -f $fasta \\
         -o ${prefix}.vcf.gz \\
         $bam

diff --git a/modules/nf-core/lofreq/call/meta.yml b/modules/nf-core/lofreq/call/meta.yml
@@ -23,6 +23,10 @@ input:
       type: file
       description: BAM input file
       pattern: "*.{bam}"
+  - intervals:
+      type: file
+      description: BED file containing target regions for variant calling
+      pattern: "*.{bed}"
   - fasta:
       type: file
       description: The reference fasta file

diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf
@@ -8,7 +8,7 @@ process LOFREQ_CALLPARALLEL {
         'biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai), path(intervals)
     path fasta
     path fai
 
@@ -22,11 +22,13 @@ process LOFREQ_CALLPARALLEL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def options_intervals = intervals ? "-l ${intervals}" : ""
     """
     lofreq \\
         call-parallel \\
         --pp-threads $task.cpus \\
         $args \\
+        $options_intervals \\
         -f $fasta \\
         -o ${prefix}.vcf.gz \\
         $bam

diff --git a/modules/nf-core/lofreq/callparallel/meta.yml b/modules/nf-core/lofreq/callparallel/meta.yml
@@ -1,6 +1,8 @@
 name: lofreq_callparallel
 description: It predicts variants using multiple processors
 keywords:
+  - variant calling
+  - low frequency variant calling
   - call
   - variants
 tools:
@@ -25,6 +27,10 @@ input:
       type: file
       description: BAM index file
       pattern: "*.{bai}"
+  - intervals:
+      type: file
+      description: BED file containing target regions for variant calling
+      pattern: "*.{bed}"
   - fasta:
       type: file
       description: Reference genome FASTA file

diff --git a/tests/modules/nf-core/lofreq/call/main.nf b/tests/modules/nf-core/lofreq/call/main.nf
@@ -7,7 +7,18 @@ include { LOFREQ_CALL } from '../../../../../modules/nf-core/lofreq/call/main.nf
 workflow test_lofreq_call {
 
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+              [] ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    LOFREQ_CALL ( input, fasta )
+}
+
+workflow test_lofreq_call_intervals {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test_bed']) ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     LOFREQ_CALL ( input, fasta )

diff --git a/tests/modules/nf-core/lofreq/call/test.yml b/tests/modules/nf-core/lofreq/call/test.yml
@@ -9,3 +9,15 @@
         [
           '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
         ]
+
+- name: lofreq call test_lofreq_call_intervals
+  command: nextflow run ./tests/modules/nf-core/lofreq/call -entry test_lofreq_call_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/call/nextflow.config
+  tags:
+    - lofreq
+    - lofreq/call
+  files:
+    - path: output/lofreq/test.vcf.gz
+      contains:
+        [
+          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
+        ]
diff --git a/tests/modules/nf-core/lofreq/callparallel/main.nf b/tests/modules/nf-core/lofreq/callparallel/main.nf
@@ -5,14 +5,29 @@ nextflow.enable.dsl = 2
 include { LOFREQ_CALLPARALLEL } from '../../../../../modules/nf-core/lofreq/callparallel/main.nf'
 
 workflow test_lofreq_callparallel {
-    
+
     input = [ [ id:'test' ], // meta map
               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              []
     ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     LOFREQ_CALLPARALLEL ( input, fasta, fai )
 }
+
+workflow test_lofreq_callparallel_intervals {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test_bed'])
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    LOFREQ_CALLPARALLEL ( input, fasta, fai )
+}
diff --git a/tests/modules/nf-core/lofreq/callparallel/test.yml b/tests/modules/nf-core/lofreq/callparallel/test.yml
@@ -9,3 +9,15 @@
         [
           '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
         ]
+
+- name: lofreq callparallel test_lofreq_callparallel_intervals
+  command: nextflow run ./tests/modules/nf-core/lofreq/callparallel -entry test_lofreq_callparallel_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/callparallel/nextflow.config
+  tags:
+    - lofreq/callparallel
+    - lofreq
+  files:
+    - path: output/lofreq/test.vcf.gz
+      contains:
+        [
+          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
+        ]