Merge branch 'master' into bump/picard

modules/cnvkit/batch/main.nf

@@ -10,6 +10,7 @@ process CNVKIT_BATCH {
     input:
     tuple val(meta), path(tumor), path(normal)
     path  fasta
+    path  fasta_fai
     path  targets
     path  reference
 
@@ -28,48 +29,167 @@ process CNVKIT_BATCH {
     script:
     def args = task.ext.args ?: ''
 
-    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
+    def tumor_exists = tumor ? true : false
-    // input pair is assumed to have same extension if both exist
+    def normal_exists = normal ? true : false
-    def is_cram = tumor.Extension == "cram" ? true : false
+
-    def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
+    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
+    def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
+    def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
+    def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
+    def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
+
+    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
 
-    // do not run samtools on normal samples in tumor_only mode
-    def normal_exists = normal ? true: false
     // tumor_only mode does not need fasta & target
     // instead it requires a pre-computed reference.cnn which is built from fasta & target
     def (normal_out, normal_args, fasta_args) = ["", "", ""]
+    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
 
     if (normal_exists){
         def normal_prefix = normal.BaseName
-        normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
+        normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
-        normal_args = normal_prefix ? "--normal $normal_out" : ""
         fasta_args = fasta ? "--fasta $fasta" : ""
+
+        // germline mode
+        // normal samples must be input without a flag
+        // requires flag --normal to be empty []
+        if(!tumor_exists){
+            tumor_out = "${normal_prefix}" + ".bam"
+            normal_args = "--normal "
+        }
+        // somatic mode
+        else {
+            normal_args = normal_prefix ? "--normal $normal_out" : ""
+        }
     }
 
     def target_args = targets ? "--targets $targets" : ""
     def reference_args = reference ? "--reference $reference" : ""
 
-    """
+    // somatic_mode cram_input
-    if $is_cram; then
+    if (tumor_cram && normal_cram){
-        samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
+        """
-        if $normal_exists; then
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
-            samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
-        fi
-    fi
 
-    cnvkit.py \\
+        cnvkit.py \\
-        batch \\
+            batch \\
-        $tumor_out \\
+            $tumor_out \\
-        $normal_args \\
+            $normal_args \\
-        $fasta_args \\
+            $fasta_args \\
-        $reference_args \\
+            $reference_args \\
-        $target_args \\
+            $target_args \\
-        --processes $task.cpus \\
+            --processes $task.cpus \\
-        $args
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // somatic_mode bam_input
+    else if (tumor_bam && normal_bam){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only_mode cram_input
+    else if(tumor_cram && !normal_exists){
+        """
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only bam_input
+    else if(tumor_bam && !normal_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode cram_input
+    // normal_args must be --normal []
+    else if (normal_cram && !tumor_exists){
+        """
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode bam_input
+    else if (normal_bam && !tumor_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
-    END_VERSIONS
-    """
 }

modules/cnvkit/batch/meta.yml

@@ -29,6 +29,10 @@ input:
       type: file
       description: |
         Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
+  - fasta_fai:
+      type: file
+      description: |
+        Input reference genome fasta index (optional, but recommended for cram_input)
   - targetfile:
       type: file
       description: |

modules/untar/main.nf

@@ -21,12 +21,18 @@ process UNTAR {
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     untar     = archive.toString() - '.tar.gz'
+
     """
+    mkdir output
+
     tar \\
+        -C output --strip-components 1 \\
         -xzvf \\
         $args \\
         $archive \\
-        $args2 \\
+        $args2
+
+    mv output ${untar}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/config/test_data.config

@@ -23,6 +23,8 @@ params {
                 test_bed12                                     = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
                 baits_bed                                      = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
 
+                reference_cnn                                  = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn"
+
                 kraken2                                        = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
@@ -146,6 +148,7 @@ params {
                 genome_21_multi_interval_bed_gz                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
                 genome_21_multi_interval_bed_gz_tbi            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
                 genome_21_chromosomes_dir                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
+                genome_21_reference_cnn                        = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
 
                 dbsnp_146_hg38_elsites                         = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
                 dbsnp_146_hg38_vcf_gz                          = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
@@ -323,6 +326,8 @@ params {
                 test_sv_vcf                                   =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
 
                 test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
+
+                test_flowcell                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
             }
             'pacbio' {
                 primers                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
@@ -415,9 +420,6 @@ params {
             'txt' {
                 hello                           = "${test_data_dir}/generic/txt/hello.txt"
             }
-            'cnn' {
-                reference                       = "${test_data_dir}/generic/cnn/reference.cnn"
-            }
             'cooler'{
                 test_pairix_pair_gz             = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
                 test_pairix_pair_gz_px2         = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"

tests/modules/cnvkit/batch/main.nf

@@ -5,8 +5,9 @@ nextflow.enable.dsl = 2
 include { CNVKIT_BATCH as CNVKIT_HYBRID    } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
 
-workflow test_cnvkit_hybrid {
+workflow test_cnvkit_hybrid_somatic {
 
     input = [
         [ id:'test' ], // meta map
@@ -16,10 +17,10 @@ workflow test_cnvkit_hybrid {
     fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
 
-    CNVKIT_HYBRID ( input, fasta, targets, [] )
+    CNVKIT_HYBRID ( input, fasta, [], targets, [] )
 }
 
-workflow test_cnvkit_wgs {
+workflow test_cnvkit_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
@@ -28,42 +29,71 @@ workflow test_cnvkit_wgs {
     ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, [], [], [] )
 }
 
-workflow test_cnvkit_cram {
+workflow test_cnvkit_cram_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
     ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
 }
 
-workflow test_cnvkit_tumoronly {
+
+workflow test_cnvkit_tumoronly_hybrid_bam {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
         []
     ]
-    reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, [], [], reference )
+    CNVKIT_TUMORONLY ( input, [], [],  [], reference )
 }
 
-workflow test_cnvkit_tumoronly_cram {
+workflow test_cnvkit_tumoronly_hybrid_cram {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
         []
     ]
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, fasta, [], reference )
+    CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
+}
+
+workflow test_cnvkit_germline_hybrid_cram {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets,  [])
+}
+
+workflow test_cnvkit_germline_hybrid_bam {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, [], targets,  [])
 }

tests/modules/cnvkit/batch/test.yml

@@ -1,5 +1,5 @@
-- name: cnvkit batch test_cnvkit_hybrid
+- name: cnvkit batch test_cnvkit_hybrid_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -26,8 +26,8 @@
     - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
       md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
 
-- name: cnvkit batch test_cnvkit_wgs
+- name: cnvkit batch test_cnvkit_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -56,8 +56,8 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_cram
+- name: cnvkit batch test_cnvkit_cram_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -86,22 +86,98 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_tumoronly
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
   files:
-    - path: output/cnvkit/reference.antitarget-tmp.bed
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
-    - path: output/cnvkit/reference.target-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
-- name: cnvkit batch test_cnvkit_tumoronly_cram
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
   files:
-    - path: output/cnvkit/reference.antitarget-tmp.bed
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
-    - path: output/cnvkit/reference.target-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_cram
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_bam
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f

tests/modules/untar/main.nf

@@ -12,3 +12,13 @@ workflow test_untar {
 
     UNTAR ( input )
 }
+
+
+workflow test_untar_different_output_path {
+    input = [
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+    ]
+
+    UNTAR ( input )
+}

tests/modules/untar/test.yml

@@ -1,5 +1,5 @@
-- name: untar
+- name: untar test_untar
-  command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
+  command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
   tags:
     - untar
   files:
@@ -9,3 +9,11 @@
       md5sum: a033d00cf6759407010b21700938f543
     - path: output/untar/kraken2/taxo.k2d
       md5sum: 094d5891cdccf2f1468088855c214b2c
+
+- name: untar test_untar_different_output_path
+  command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
+  tags:
+    - untar
+  files:
+    - path: output/untar/flowcell/RunInfo.xml
+      md5sum: 03038959f4dd181c86bc97ae71fe270a