Nanomonsv get

modules/nf-core/nanomonsv/get/main.nf

@@ -0,0 +1,61 @@
+// 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/nf-core/
+//               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 NANOMONSV_GET {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "bioconda::nanomonsv=0.5.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nanomonsv:0.5.0--pyhdfd78af_0':
+        'quay.io/biocontainers/nanomonsv:0.5.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(parse_intermediates), path(control_bam), path(control_bai), path(control_parse_intermediates)
+    path reference_fasta
+
+    output:
+    tuple val(meta), path("${prefix}.nanomonsv.result.vcf")         , emit: vcf
+    tuple val(meta), path("${prefix}.nanomonsv.result.txt")         , emit: text_report
+    tuple val(meta), path("${prefix}.nanomonsv.supporting_read.txt"), emit: supp_read
+    path "versions.yml"                                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def control_prefix = task.ext.control_prefix ?: "${meta.id}"
+    if (control_prefix) {
+        args += " --control_prefix ${control_prefix} --control_bam ${control_bam}"
+    }
+    """
+    nanomonsv get ${args} ${prefix} \
+        ${bam} ${reference_fasta}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanomonsv: \$(echo \$(nanomonsv --version 2>&1) | sed 's/^nanomonsv //')
+        mafft: \$(echo \$(mafft --version 2>&1) | sed 's/^v//; s/ (.*//')
+        racon: \$(echo \$(racon --version 2>&1) | sed 's/^v//')
+        tabix: \$(echo \$(tabix --version 2>&1) | sed 's/^tabix (htslib) //; s/ Copyright.*//')
+        bgzip: \$(echo \$(bgzip --version 2>&1) | sed 's/^bgzip (htslib) //; s/ Copyright.*//')
+        python: \$(python3 --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+}

modules/nf-core/nanomonsv/get/meta.yml

@@ -0,0 +1,51 @@
+name: "nanomonsv_get"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "nanomonsv":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Python tools for detecting structural variation from nanopore sequence data"
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      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 ]
+  #
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## 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 ]
+  #
+  - 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:
+  - "@awgymer"

tests/config/pytest_modules.yml

@@ -2151,6 +2151,10 @@ nanolyse:
   - modules/nf-core/nanolyse/**
   - tests/modules/nf-core/nanolyse/**
 
+nanomonsv/get:
+  - modules/nf-core/nanomonsv/get/**
+  - tests/modules/nf-core/nanomonsv/get/**
+
 nanomonsv/parse:
   - modules/nf-core/nanomonsv/parse/**
   - tests/modules/nf-core/nanomonsv/parse/**

tests/modules/nf-core/nanomonsv/get/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NANOMONSV_GET } from '../../../../../modules/nf-core/nanomonsv/get/main.nf'
+
+workflow test_nanomonsv_get {
+
+    def data_path = 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/nanomonsv'
+    input = channel.of([
+        [ id:'test' ], // meta map
+        file("${data_path}/input_bam/test_tumor.bam", checkIfExists: true),
+        file("${data_path}/input_bam/test_tumor.bam.bai", checkIfExists: true),
+        file("${data_path}/parse_output/test_tumor/*.gz*"),
+        file("${data_path}/input_bam/test_ctrl.bam", checkIfExists: true),
+        file("${data_path}/input_bam/test_ctrl.bam.bai", checkIfExists: true),
+        file("${data_path}/parse_output/test_ctrl/*.gz*"),
+    ])
+    ref = file('s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa')
+
+    NANOMONSV_GET ( input, ref )
+}

tests/modules/nf-core/nanomonsv/get/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'NANOMONSV_GET' {
+        ext.prefix = { "${meta.id}_tumor" }
+        ext.control_prefix = { "${meta.id}_ctrl" }
+    }
+}

tests/modules/nf-core/nanomonsv/get/test.yml

@@ -0,0 +1,15 @@
+- name: nanomonsv get test_nanomonsv_get
+  command: nextflow run ./tests/modules/nf-core/nanomonsv/get -entry test_nanomonsv_get -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nanomonsv/get/nextflow.config
+  tags:
+    - nanomonsv
+    - nanomonsv/get
+  files:
+    - path: output/nanomonsv/test_tumor.nanomonsv.result.txt
+      md5sum: 4093bd514c334059b91d77b084de961d
+    - path: output/nanomonsv/test_tumor.nanomonsv.result.vcf
+      contains:
+        - "chr18\t68712223\td_2\tC\t<DEL>\t.\tPASS\tEND=68715588;SVTYPE=DEL;SVLEN=-3365\tTR:VR\t25:4\t24:0\n"
+    - path: output/nanomonsv/test_tumor.nanomonsv.supporting_read.txt
+      contains:
+        - "chr10\t87940538\t+\tchr10\t87952584\t-\tATAGAGATTATACTTTGTGTA\tr_0\t37b0700e-96e1-4d0c-9299-18eabf25515d\t13944\t+"
+    - path: output/nanomonsv/versions.yml