fix optional cram support in modules and migrate to nf-test

modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf

@@ -24,6 +24,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = input.collect(){"--INPUT $it"}.join(" ")
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
 
     def avail_mem = 3072
     if (!task.memory) {
@@ -36,7 +37,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
         EstimateLibraryComplexity \\
         $input_list \\
         --OUTPUT ${prefix}.metrics \\
-        --REFERENCE_SEQUENCE ${fasta} \\
+        $reference \\
         --TMP_DIR . \\
         $args
 

modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test

@@ -0,0 +1,113 @@
+nextflow_process {
+
+    name "Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY"
+    script "../main.nf"
+    process "GATK4_ESTIMATELIBRARYCOMPLEXITY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/estimatelibrarycomplexity"
+
+    test("homo_sapiens - bam") {
+
+        when {
+            process {
+                """
+                // [ meta, input ]
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true)
+                ]
+                // fasta
+                input[1] = []
+                // fai
+                input[2] = []
+                // dict
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict' , checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                            file(process.out.metrics[0][1]).name,
+                            process.out.versions
+                        ).match()
+                }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - cram") {
+
+        when {
+            process {
+                """
+                // [ meta, input ]
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ]
+                // fasta
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' , checkIfExists: true)
+                // fai
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' , checkIfExists: true)
+                // dict
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict' , checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                            file(process.out.metrics[0][1]).name,
+                            process.out.versions
+                        ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // [ meta, input ]
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true)
+                ]
+                // fasta
+                input[1] = []
+                // fai
+                input[2] = []
+                // dict
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict' , checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                            file(process.out.metrics[0][1]).name,
+                            process.out.versions
+                        ).match()
+                }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gatk4/estimatelibrarycomplexity/tests/tags.yml

@@ -0,0 +1,2 @@
+gatk4/estimatelibrarycomplexity:
+  - "modules/nf-core/gatk4/estimatelibrarycomplexity/**"

modules/nf-core/picard/addorreplacereadgroups/main.nf

@@ -8,7 +8,7 @@ process PICARD_ADDORREPLACEREADGROUPS {
         'biocontainers/picard:3.1.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(reads)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fasta_index)
 
@@ -24,26 +24,24 @@ process PICARD_ADDORREPLACEREADGROUPS {
     script:
     def args = task.ext.args        ?: ''
     def prefix = task.ext.prefix    ?: "${meta.id}"
-    def suffix = task.ext.suffix    ?: "${bam.getExtension()}"
+    def suffix = task.ext.suffix    ?: "${reads.getExtension()}"
     def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
-    def create_index = ( suffix == "bam" )? "--CREATE_INDEX" : ""
     def avail_mem = 3072
     if (!task.memory) {
         log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
     } else {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
 
-    if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
     """
     picard \\
         -Xmx${avail_mem}M \\
         AddOrReplaceReadGroups \\
         $args \\
         $reference \\
-        $create_index \\
-        --INPUT ${bam} \\
+        --INPUT ${reads} \\
         --OUTPUT ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
@@ -54,15 +52,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
 
     stub:
     def prefix = task.ext.prefix    ?: "${meta.id}"
-    def suffix = task.ext.suffix    ?: "${bam.getExtension()}"
-    if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-    def create_index = ""
-    if (suffix == "bam") {
-        create_index = "touch ${prefix}.${suffix}.bai"
-    }
+    def suffix = task.ext.suffix    ?: "${reads.getExtension()}"
+    if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.${suffix}
-    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/picard/addorreplacereadgroups/meta.yml

@@ -30,10 +30,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - reads:
       type: file
-      description: Input BAM file
-      pattern: "*.{bam}"
+      description: Sequence reads file, can be SAM/BAM/CRAM format
+      pattern: "*.{bam,cram,sam}"
   - fasta:
       type: file
       description: Reference genome file

modules/nf-core/picard/addorreplacereadgroups/tests/bam.config

@@ -2,6 +2,7 @@ process {
     withName: 'PICARD_ADDORREPLACEREADGROUPS'{
         ext.prefix = { "${meta.id}.replaced"}
         ext.args = {[
+            "--CREATE_INDEX",
             "-LB ${meta.id}",
             "-PL ILLUMINA",
             "-PU bc1",

modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test

@@ -26,8 +26,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("bam_name") },
-                { assert snapshot(file(process.out.bai[0][1]).name).match("bai_name") },
+                { assert snapshot(
+                            file(process.out.bam[0][1]).name,
+                            file(process.out.bai[0][1]).name,
+                            process.out.versions
+                        ).match()
+                },
             )
         }
 
@@ -53,8 +57,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.cram[0][1]).name).match("cram_name") },
-                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(
+                            file(process.out.cram[0][1]).name,
+                            process.out.versions
+                        ).match()
+                },
             )
         }