Merge branch 'master' into add_compression_to_bam2fq

modules/gatk4/mergebamalignment/main.nf

@@ -43,4 +43,15 @@ process GATK4_MERGEBAMALIGNMENT {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/gatk4/mutect2/main.nf

@@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.vcf.gz.stats
+    touch ${prefix}.f1r2.tar.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/gatk4/revertsam/main.nf

@@ -39,4 +39,15 @@ process GATK4_REVERTSAM {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.reverted.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/gatk4/samtofastq/main.nf

@@ -40,4 +40,17 @@ process GATK4_SAMTOFASTQ {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+    touch ${prefix}_1.fastq.gz
+    touch ${prefix}_2.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/view/main.nf

@@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

tests/modules/gatk4/mergebamalignment/main.nf

@@ -14,3 +14,14 @@ workflow test_gatk4_mergebamalignment {
 
     GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }
+
+workflow test_gatk4_mergebamalignment_stubs {
+     input    = [ [ id:'test' ], // meta map
+                 "test_foo.bam",
+                 "test_bar.bam"
+               ]
+    fasta    = "genome.fasta"
+    dict     = "genome.fasta.dict"
+
+    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
+}

tests/modules/gatk4/mergebamalignment/test.yml

@@ -7,3 +7,12 @@
     - path: output/gatk4/test.bam
       md5sum: e6f1b343700b7ccb94e81ae127433988
     - path: output/gatk4/versions.yml
+
+- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
+  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mergebamalignment
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml

tests/modules/gatk4/mutect2/main.nf

@@ -118,3 +118,25 @@ workflow test_gatk4_mutect2_mitochondria {
 
     GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
 }
+
+workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
+    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ "foo_paired.bam",
+                "foo_paired2.bam"
+                ],
+              [ "foo_paired.bam.bai",
+                "foo_paired2.bam.bai"
+                ],
+              []
+            ]
+
+    fasta = "genome.fasta"
+    fai = "genome.fasta.fai"
+    dict = "genome.fasta.dict"
+    germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
+    germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
+    panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
+    panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
+
+    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}

tests/modules/gatk4/mutect2/test.yml

@@ -69,3 +69,15 @@
       md5sum: fc6ea14ca2da346babe78161beea28c9
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
+  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.f1r2.tar.gz
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml

tests/modules/gatk4/revertsam/main.nf

@@ -11,3 +11,11 @@ workflow test_gatk4_revertsam {
 
     GATK4_REVERTSAM ( input )
 }
+
+workflow test_gatk4_revertsam_stubs {
+    input = [ [ id:'test' ], // meta map
+              "foo_paired_end.bam"
+            ]
+
+    GATK4_REVERTSAM ( input )
+}

tests/modules/gatk4/revertsam/test.yml

@@ -7,3 +7,12 @@
     - path: output/gatk4/test.reverted.bam
       md5sum: f783a88deb45c3a2c20ca12cbe1c5652
     - path: output/gatk4/versions.yml
+
+- name: gatk4 revertsam test_gatk4_revertsam_stubs
+  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/revertsam
+  files:
+    - path: output/gatk4/test.reverted.bam
+    - path: output/gatk4/versions.yml

tests/modules/gatk4/samtofastq/main.nf

@@ -19,3 +19,11 @@ workflow test_gatk4_samtofastq_paired_end {
 
     GATK4_SAMTOFASTQ ( input )
 }
+
+workflow test_gatk4_samtofastq_paired_end_stubs {
+    input = [ [ id:'test', single_end: false ], // meta map
+              [ "foo_paired_end.bam" ]
+            ]
+
+    GATK4_SAMTOFASTQ ( input )
+}

tests/modules/gatk4/samtofastq/test.yml

@@ -19,3 +19,13 @@
     - path: output/gatk4/test_2.fastq.gz
       md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
     - path: output/gatk4/versions.yml
+
+- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
+  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/samtofastq
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+    - path: output/gatk4/test_2.fastq.gz
+    - path: output/gatk4/versions.yml

tests/modules/samtools/view/main.nf

@@ -22,3 +22,12 @@ workflow test_samtools_view_cram {
 
     SAMTOOLS_VIEW ( input, fasta )
 }
+
+workflow test_samtools_view_stubs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                "foo_paired_end.bam",
+                []
+            ]
+
+    SAMTOOLS_VIEW ( input, [] )
+}

tests/modules/samtools/view/test.yml

@@ -14,3 +14,11 @@
     - samtools
   files:
     - path: output/samtools/test.cram
+
+- name: samtools view test_samtools_view_stubs
+  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam