rhocall

modules/rhocall/annotate/main.nf

@@ -1,75 +1,51 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process RHOCALL_ANNOTATE {
     tag "$meta.id"
     label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+        'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0':
-        'quay.io/biocontainers/YOUR-TOOL-HERE' }"
+        'quay.io/biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    tuple val(meta), path(vcf), path(tbi)
-    //               MUST be provided as an input via a Groovy Map called "meta".
+    tuple val(meta), path(roh)
-    //               This information may not be required in some instances e.g. indexing reference genome files:
+    path bed
-    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*_rhocall.vcf"), emit: vcf
-    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"                   , emit: versions
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    def az_bed = bed ? "-b ${bed}" : ''
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
+    rhocall \\
-        sort \\
+        annotate \\
         $args \\
-        -@ $task.cpus \\
+        $az_bed \\
-        -o ${prefix}.bam \\
+        -r $roh \\
-        -T $prefix \\
+        -o ${prefix}_rhocall.vcf \\
-        $bam
+        $vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rhocall: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_rhocall.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ))
     END_VERSIONS
     """
 }

modules/rhocall/annotate/meta.yml

@@ -1,11 +1,10 @@
 name: "rhocall_annotate"
-## TODO nf-core: Add a description of the module and list keywords
+description: "Markup VCF file using rho-calls."
-description: write your description here
 keywords:
-  - sort
+  - roh
+  - rhocall
 tools:
   - "rhocall":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "Call regions of homozygosity and make tentative UPD calls."
       homepage: "https://github.com/dnil/rhocall"
       documentation: "https://github.com/dnil/rhocall"
@@ -13,39 +12,43 @@ tools:
       doi: ""
       licence: "['GPL v3']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+  - vcf:
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: vcf file
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.{vcf,vcf.gz}"
+  - tbi:
+      type: file
+      description: vcf index file
+      pattern: "*.{tbi}"
+  - roh:
+      type: file
+      description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL
+      pattern: "*.{roh}"
+  - bed:
+      type: file
+      description: BED file with AZ windows.
+      pattern: "*.{bed}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+  - vcf:
+      type: file
+      description: vcf file
+      pattern: "*.{vcf,vcf.gz}"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
 
 authors:
   - "@ramprasadn"

tests/modules/rhocall/annotate/main.nf

@@ -3,13 +3,38 @@
 nextflow.enable.dsl = 2
 
 include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf'
+include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
 
 workflow test_rhocall_annotate {
 
-    input = [
+    input = [ [ id:'test' ], // meta map
-        [ id:'test', single_end:false ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-    ]
+
+    af_file = []
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
+
+}
+
+workflow test_rhocall_annotate_stub {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = []
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
 
-    RHOCALL_ANNOTATE ( input )
 }

tests/modules/rhocall/annotate/test.yml

@@ -1,14 +1,17 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml rhocall/annotate
 - name: "rhocall annotate"
   command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config
   tags:
     - "rhocall"
-    #
     - "rhocall/annotate"
-    #
   files:
-    - path: "output/rhocall/test.bam"
+    - path: "output/rhocall/test_rhocall.vcf"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: "output/rhocall/versions.yml"
-    - path: output/rhocall/versions.yml
+
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+- name: "rhocall annotate stub"
+  command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config -stub-run
+  tags:
+    - "rhocall"
+    - "rhocall/annotate"
+  files:
+    - path: "output/rhocall/test_rhocall.vcf"
+    - path: "output/rhocall/versions.yml"