Merge branch 'master' into cnvkit_reference

modules/cnvkit/batch/main.nf

@@ -2,10 +2,10 @@ process CNVKIT_BATCH {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
+    conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' :
-        'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' :
+        'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }"
 
     input:
     tuple val(meta), path(tumor), path(normal)
@@ -18,6 +18,8 @@ process CNVKIT_BATCH {
     tuple val(meta), path("*.cnn"), emit: cnn, optional: true
     tuple val(meta), path("*.cnr"), emit: cnr, optional: true
     tuple val(meta), path("*.cns"), emit: cns, optional: true
+    tuple val(meta), path("*.pdf"), emit: pdf, optional: true
+    tuple val(meta), path("*.png"), emit: png, optional: true
     path "versions.yml"           , emit: versions
 
     when:
@@ -25,21 +27,39 @@ process CNVKIT_BATCH {
 
     script:
     def args = task.ext.args ?: ''
-    def normal_args = normal ? "--normal $normal" : ""
-    def fasta_args = fasta ? "--fasta $fasta" : ""
+
+    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
+    // input pair is assumed to have same extension if both exist
+    def is_cram = tumor.Extension == "cram" ? true : false
+    def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${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) = ["", "", ""]
+
+    if (normal_exists){
+        def normal_prefix = normal.BaseName
+        normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
+        normal_args = normal_prefix ? "--normal $normal_out" : ""
+        fasta_args = fasta ? "--fasta $fasta" : ""
+    }
+
+    def target_args = targets ? "--targets $targets" : ""
     def reference_args = reference ? "--reference $reference" : ""
 
-    def target_args = ""
-    if (args.contains("--method wgs") || args.contains("-m wgs")) {
-        target_args = targets ? "--targets $targets" : ""
-    }
-    else {
-        target_args = "--targets $targets"
-    }
     """
+    if $is_cram; then
+        samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
+        if $normal_exists; then
+            samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
+        fi
+    fi
+
     cnvkit.py \\
         batch \\
-        $tumor \\
+        $tumor_out \\
         $normal_args \\
         $fasta_args \\
         $reference_args \\

modules/cnvkit/batch/meta.yml

@@ -11,27 +11,6 @@ tools:
       homepage: https://cnvkit.readthedocs.io/en/stable/index.html
       documentation: https://cnvkit.readthedocs.io/en/stable/index.html
       licence: ["Apache-2.0"]
-params:
-  - outdir:
-      type: string
-      description: |
-        The pipeline's output directory. By default, the module will
-        output files into `$params.outdir/<SOFTWARE>`
-  - publish_dir_mode:
-      type: string
-      description: |
-        Value for the Nextflow `publishDir` mode parameter.
-        Available: symlink, rellink, link, copy, copyNoFollow, move.
-  - enable_conda:
-      type: boolean
-      description: |
-        Run the module with Conda using the software specified
-        via the `conda` directive
-  - singularity_pull_docker_container:
-      type: boolean
-      description: |
-        Instead of directly downloading Singularity images for use with Singularity,
-        force the workflow to pull and convert Docker containers instead.
 input:
   - meta:
       type: map
@@ -49,7 +28,7 @@ input:
   - fasta:
       type: file
       description: |
-        Input reference genome fasta file
+        Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
   - targetfile:
       type: file
       description: |
@@ -80,6 +59,14 @@ output:
       type: file
       description: File containing copy number segment information
       pattern: "*.{cns}"
+  - pdf:
+      type: file
+      description: File with plot of copy numbers or segments on chromosomes
+      pattern: "*.{pdf}"
+  - png:
+      type: file
+      description: File with plot of bin-level log2 coverages and segmentation calls
+      pattern: "*.{png}"
   - versions:
       type: file
       description: File containing software versions
@@ -91,3 +78,4 @@ authors:
   - "@drpatelh"
   - "@fbdtemme"
   - "@lassefolkersen"
+  - "@SusiJo"

tests/modules/cnvkit/batch/main.nf

@@ -35,8 +35,8 @@ workflow test_cnvkit_cram {
 
     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']['test_paired_end_sorted_bam'], checkIfExists: true)
+        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)
 
@@ -50,8 +50,20 @@ workflow test_cnvkit_tumoronly {
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
         []
     ]
-    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
 
     CNVKIT_TUMORONLY ( input, [], [], reference )
 }
+
+workflow test_cnvkit_tumoronly_cram {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_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)
+
+    CNVKIT_TUMORONLY ( input, fasta, [], reference )
+}

tests/modules/cnvkit/batch/test.yml

@@ -1,15 +1,14 @@
 - name: cnvkit batch test_cnvkit_hybrid
   command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
-    - cnvkit/batch
     - cnvkit
+    - cnvkit/batch
   files:
     - path: output/cnvkit/baits.antitarget.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvkit/baits.target.bed
       md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
     - path: output/cnvkit/reference.cnn
-      md5sum: ac99c1ad8b917b96ae15119146c91ab9
+      md5sum: 035d031f54c5f1b43b903da96559b475
     - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test.paired_end.sorted.bintest.cns
@@ -30,17 +29,16 @@
 - name: cnvkit batch test_cnvkit_wgs
   command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
-    - cnvkit/batch
     - cnvkit
+    - cnvkit/batch
   files:
     - path: output/cnvkit/genome.antitarget.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvkit/genome.bed
       md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
     - path: output/cnvkit/genome.target.bed
       md5sum: a13353ae9c8405e701390c069255bbd2
     - path: output/cnvkit/reference.cnn
-      md5sum: 05c6211e0179885b8a83e44fd21d5f86
+      md5sum: 1606a85410bfaa79464be6e98699aa83
     - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
@@ -61,17 +59,16 @@
 - name: cnvkit batch test_cnvkit_cram
   command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
-    - cnvkit/batch
     - cnvkit
+    - cnvkit/batch
   files:
     - path: output/cnvkit/genome.antitarget.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvkit/genome.bed
       md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
     - path: output/cnvkit/genome.target.bed
       md5sum: a13353ae9c8405e701390c069255bbd2
     - path: output/cnvkit/reference.cnn
-      md5sum: 05c6211e0179885b8a83e44fd21d5f86
+      md5sum: 1606a85410bfaa79464be6e98699aa83
     - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
@@ -92,10 +89,19 @@
 - name: cnvkit batch test_cnvkit_tumoronly
   command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
-    - cnvkit/batch
     - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/reference.antitarget-tmp.bed
+    - path: output/cnvkit/reference.target-tmp.bed
+      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+
+- name: cnvkit batch test_cnvkit_tumoronly_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
+  tags:
+    - cnvkit
+    - cnvkit/batch
   files:
     - path: output/cnvkit/reference.antitarget-tmp.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvkit/reference.target-tmp.bed
       md5sum: 26d25ff2d6c45b6d92169b3559c6acdb