Add GATK indelrealigner tests

modules/gatk/indelrealigner/main.nf

@@ -22,11 +22,12 @@ process GATK_INDELREALIGNER {
     task.ext.when == null || task.ext.when
 
     script:
-    if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def known = known_vcf ? "-known ${known_vcf}" : ""
 
+    if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     def avail_mem = 3
     if (!task.memory) {
         log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -39,9 +40,8 @@ process GATK_INDELREALIGNER {
         -Xmx${avail_mem}g \\
         -T IndelRealigner \\
         -R ${fasta} \\
-        -nt ${task.cpus}
         -I ${input} \\
-        -targetIntervals ${intervals} \\
+        --targetIntervals ${intervals} \\
         ${known} \\
         -o ${prefix}.bam \\
         $args

tests/modules/gatk/indelrealigner/main.nf

@@ -2,21 +2,32 @@
 
 nextflow.enable.dsl = 2
 
+include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
 include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
 
-// TODO add REalignerTargetCrator
-
 
 workflow test_gatk_indelrealigner {
 
-    input = [
+
-        [ id:'test', single_end:false ], // meta map
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bai'], checkIfExists: true),
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-        GATK_REALIGNERTARGETCREATOR.out.intervals
+
+    input_realignertargetcreator     = [ [ 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),
                 ]
 
-    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
 
-    GATK_INDELREALIGNER ( input, reference, [] )
+    ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
+
+    ch_bams_indelrealigner = Channel.of([ [ 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)
+                ])
+
+    ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
+
+    GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
 }

tests/modules/gatk/indelrealigner/nextflow.config

@@ -1,6 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    ext.prefix = "${meta.id}.realigned"
+    ext.prefix = { "${meta.id}.realigned" }
 
 }

tests/modules/gatk/indelrealigner/test.yml

@@ -1,14 +1,12 @@
-## TODO nf-core: Please run the following command to build this file:
+- name: gatk indelrealigner test_gatk_indelrealigner
-#                nf-core modules create-test-yml gatk/indelrealigner
-- name: "gatk indelrealigner"
   command: nextflow run ./tests/modules/gatk/indelrealigner -entry test_gatk_indelrealigner -c ./tests/config/nextflow.config  -c ./tests/modules/gatk/indelrealigner/nextflow.config
   tags:
-    - "gatk"
+    - gatk/indelrealigner
-    #
+    - gatk
-    - "gatk/indelrealigner"
-    #
   files:
-    - path: "output/gatk/test.bam"
+    - path: output/gatk/test.realigned.bai
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+      md5sum: 85a67df8827fe426e7f3a458134c0551
-    - path: output/gatk/versions.yml
+    - path: output/gatk/test.realigned.bam
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: ea1df6f7fcafc408fae4dc1574813d8a
+    - path: output/gatk/test.realigned.intervals
+      md5sum: 7aa7a1b235a510e6591e262382086bf8