Update lofreq somatic and callparallel

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), path(intervals)
+    tuple val(meta), path(tumor), path(tumor_index), path(intervals)
     path fasta
     path fai
 
@@ -23,15 +23,25 @@ process LOFREQ_CALLPARALLEL {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_intervals = intervals ? "-l ${intervals}" : ""
+
+    def tumor_cram =  tumor.Extension == "cram" ? true : false
+    def tumor_bam = tumor.Extension == "bam" ? true : false
+    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
+
+    def samtools_cram_convert = ''
+    samtools_cram_convert += tumor_cram ? "    samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out\n" : ''
+    samtools_cram_convert += tumor_cram ? "    samtools index $tumor_out\n" : ''
     """
+    $samtools_cram_convert
+
     lofreq \\
         call-parallel \\
         --pp-threads $task.cpus \\
         $args \\
         $options_intervals \\
         -f $fasta \\
         -o ${prefix}.vcf.gz \\
-        $bam
+        $tumor_out
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/lofreq/callparallel/meta.yml

@@ -18,11 +18,11 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - bam:
+  - tumor:
       type: file
       description: Sorted BAM file
       pattern: "*.{bam}"
-  - bai:
+  - tumor_index:
       type: file
       description: BAM index file
       pattern: "*.{bai}"
@@ -58,3 +58,5 @@ authors:
 maintainers:
   - "@kaurravneet4123"
   - "@bjohnnyd"
+  - "@nevinwu"
+  - "@AitorPeseta"

modules/nf-core/lofreq/somatic/main.nf

@@ -1,14 +1,13 @@
 process LOFREQ_SOMATIC {
     tag "$meta.id"
-    label "process_high"
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
         'biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
-
     input:
-    tuple val(meta), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai), path(target_bed)
+    tuple val(meta), path(tumor), path(tumor_index), path(normal), path(normal_index), path(target_bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
@@ -23,14 +22,28 @@ process LOFREQ_SOMATIC {
     def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_target_bed = target_bed ? "-l ${target_bed}" : ""
+
+    def tumor_cram =  tumor.Extension == "cram" ? true : false
+    def normal_cram =  normal.Extension == "cram" ? true : false
+
+    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
+    def normal_out = normal_cram ? normal.BaseName + ".bam" : "${normal}"
+
+    def samtools_cram_convert = ''
+    samtools_cram_convert += normal_cram ? "    samtools view -T $fasta $normal -@ $task.cpus -o $normal_out\n" : ''
+    samtools_cram_convert += normal_cram ? "    samtools index $normal_out\n" : ''
+    samtools_cram_convert += tumor_cram ? "    samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out\n" : ''
+    samtools_cram_convert += tumor_cram ? "    samtools index $tumor_out\n" : ''
     """
+    $samtools_cram_convert
+
     lofreq \\
         somatic \\
         --threads $task.cpus \\
         $args \\
         -f $fasta \\
-        -t $tumor_bam \\
-        -n $normal_bam \\
+        -t $tumor_out \\
+        -n $normal_out \\
         ${options_target_bed} \\
         -o ${prefix}
 

modules/nf-core/lofreq/somatic/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: https://csb5.github.io/lofreq/
       documentation: https://csb5.github.io/lofreq/commands/
       doi: 10.1093/nar/gks918
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -23,19 +23,19 @@ input:
   - meta3:
       type: map
       description: Groovy Map containing reference information
-  - tumor_bam:
+  - tumor:
       type: file
       description: tumor sample input BAM file
       pattern: "*.{bam}"
-  - tumor_bai:
+  - tumor_index:
       type: file
       description: tumor sample BAM index file
       pattern: "*.{bai}"
-  - normal_bam:
+  - normal:
       type: file
       description: normal sample input BAM file
       pattern: "*.{bam}"
-  - normal_bai:
+  - normal_index:
       type: file
       description: normal sample BAM index file
       pattern: "*.{bai}"
@@ -69,3 +69,4 @@ authors:
   - "@nevinwu"
 maintainers:
   - "@nevinwu"
+  - "@AitorPeseta"