Merge remote-tracking branch 'upstream/master' into cnvkit_bam

modules/deeptools/bamcoverage/main.nf

@@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
-        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
+        'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
+    path(fasta)
+    path(fasta_fai)
 
     output:
     tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
@@ -22,16 +24,44 @@ process DEEPTOOLS_BAMCOVERAGE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
 
-    """
-    bamCoverage \\
-        --bam $input \\
-        $args \\
-        --numberOfProcessors ${task.cpus} \\
-        --outFileName ${prefix}
+    // cram_input is currently not working with deeptools
+    // therefore it's required to convert cram to bam first
+    def is_cram = input.Extension == "cram" ? true : false
+    def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
+    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
+
+    if (is_cram){
+        """
+        samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
+        samtools index -b $input_out -@ $task.cpus
+
+        bamCoverage \\
+            --bam $input_out \\
+            $args \\
+            --numberOfProcessors ${task.cpus} \\
+            --outFileName ${prefix}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
+        END_VERSIONS
+        """
+
+    }
+    else {
+        """
+        bamCoverage \\
+            --bam $input_out \\
+            $args \\
+            --numberOfProcessors ${task.cpus} \\
+            --outFileName ${prefix}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
+        END_VERSIONS
+        """
+    }
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
-    END_VERSIONS
-    """
 }

modules/deeptools/bamcoverage/meta.yml

@@ -25,6 +25,14 @@ input:
       type: file
       description: BAM/CRAM index file
       pattern: "*.{bai,crai}"
+  - fasta:
+      type: file
+      description: Reference file the CRAM file was created with (required with CRAM input)
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: file
+      description: Index of the reference file (optional, but recommended)
+      pattern: "*.{fai}"
 
 output:
   - meta:
@@ -47,3 +55,4 @@ output:
 
 authors:
   - "@FriederikeHanssen"
+  - "@SusiJo"

tests/modules/deeptools/bamcoverage/main.nf

@@ -12,7 +12,7 @@ workflow test_deeptools_bamcoverage_bam {
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
         ]
 
-    DEEPTOOLS_BAMCOVERAGE ( input )
+    DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
 }
 
 workflow test_deeptools_bamcoverage_cram {
@@ -22,6 +22,20 @@ workflow test_deeptools_bamcoverage_cram {
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], 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)
 
-    DEEPTOOLS_BAMCOVERAGE ( input )
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
+}
+
+workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
 }

tests/modules/deeptools/bamcoverage/test.yml

@@ -1,21 +1,26 @@
 - name: deeptools bamcoverage test_deeptools_bamcoverage_bam
-  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
   tags:
-    - deeptools
     - deeptools/bamcoverage
+    - deeptools
   files:
     - path: output/deeptools/test.bigWig
       md5sum: 95fe9383a9e6c02aea6b785cf074274f
-    - path: output/deeptools/versions.yml
-      md5sum: 68c94e73b7a8c0935578bad61fea54c1
 
 - name: deeptools bamcoverage test_deeptools_bamcoverage_cram
-  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
   tags:
-    - deeptools
     - deeptools/bamcoverage
+    - deeptools
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+
+- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
+  tags:
+    - deeptools/bamcoverage
+    - deeptools
   files:
     - path: output/deeptools/test.bigWig
       md5sum: 95fe9383a9e6c02aea6b785cf074274f
-    - path: output/deeptools/versions.yml
-      md5sum: 665bbd2979c49bf3974a24bd44a88e94