Revert "Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)"

This reverts commit fead37d57a.

software/msisensor/msi/functions.nf

@@ -1,60 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.args3         = args.args3 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/msisensor/msi/main.nf

@@ -1,45 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process MSISENSOR_MSI {
-    tag "$meta.id"
-    label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
-    } else {
-        container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
-    }
-
-    input:
-    tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers)
-
-    output:
-    tuple val(meta), path("${prefix}")         , emit: output
-    tuple val(meta), path("${prefix}_dis")     , emit: output_dis
-    tuple val(meta), path("${prefix}_germline"), emit: output_germline
-    tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
-    path "*.version.txt"                       , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
-    msisensor \\
-        msi \\
-        -d $homopolymers \\
-        -n $normal_bam \\
-        -t $tumor_bam \\
-        -o $prefix \\
-        $options.args
-
-    echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt
-    """
-}

software/msisensor/msi/meta.yml

@@ -1,69 +0,0 @@
-name: msisensor_msi
-
-description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
-keywords:
-  - homoploymer,microsatellite
-tools:
-  - msisensor:
-      description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
-      homepage: https://github.com/ding-lab/msisensor
-      documentation: None
-      tool_dev_url: None
-      doi: "10.1093/bioinformatics/btt755"
-      licence: ['MIT']
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - normal_bam:
-      type: file
-      description: Coordinate sorted BAM/CRAM/SAM file from normal tissue
-      pattern: "*.{bam,cram,sam}"
-  - normal_bai:
-      type: file
-      description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue
-      pattern: "*.{bam,cram,sam}"
-  - tumor_bam:
-      type: file
-      description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue
-      pattern: "*.{bam,cram,sam}"
-  - tumor_bai:
-      type: file
-      description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue
-      pattern: "*.{bam,cram,sam}"
-  - homopolymers:
-      type: file
-      description: Output file from MSIsensor scan module
-      pattern: "*.msisensor_scan.tab"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-  - txt:
-      type: file
-      description: MSIsensor MSI final report file
-      pattern: "*.output"
-  - txt:
-      type: file
-      description: MSIsensor MSI DIS report file
-      pattern: "*.output_dis"
-  - txt:
-      type: file
-      description: MSIsensor MSI germline report file
-      pattern: "*.output_germline"
-  - txt:
-      type: file
-      description: MSIsensor MSI somatic report file
-      pattern: "*.output_somatic"
-authors:
-  - "@kevbrick"

software/msisensor/scan/functions.nf

@@ -1,60 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.args3         = args.args3 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/msisensor/scan/main.nf

@@ -1,40 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process MSISENSOR_SCAN {
-    tag "$meta.id"
-    label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
-    } else {
-        container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
-    }
-
-    input:
-    tuple val(meta), path(fasta)
-
-    output:
-    tuple (val(meta), path("*.tab"), emit: txt)
-    path ("*.version.txt"          , emit: version)
-
-    script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    """
-    msisensor \\
-        scan \\
-        -d $fasta \\
-        -o ${prefix}.msisensor_scan.tab \\
-        $options.args
-
-    echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt
-    """
-}

software/msisensor/scan/meta.yml

@@ -1,42 +0,0 @@
-name: msisensor_scan
-
-description: Scan a reference genome to get microsatellite & homopolymer information
-keywords:
-  - homoploymer,microsatellite
-tools:
-  - msisensor:
-      description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
-      homepage: https://github.com/ding-lab/msisensor
-      documentation: None
-      tool_dev_url: None
-      doi: "10.1093/bioinformatics/btt755"
-      licence: ['MIT']
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fasta:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa,fasta}"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-  - txt:
-      type: file
-      description: MSIsensor scan output file of homopolymers & minisatellites
-      pattern: "*.msisensor_scan.txt"
-
-authors:
-  - "@kevbrick"

tests/config/pytest_software.yml

@@ -278,14 +278,6 @@ mosdepth:
   - software/mosdepth/**
   - tests/software/mosdepth/**
 
-msisensor_scan:
-  - software/msisensor/scan/**
-  - tests/software/msisensor/scan/**
-
-msisensor_msi:
-  - software/msisensor/msi/**
-  - tests/software/msisensor/msi/**
-
 multiqc:
   - software/fastqc/**
   - software/multiqc/**

tests/software/msisensor/msi/main.nf

@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR_SCAN } from '../../../../software/msisensor/scan/main.nf' addParams( options: [:] )
-include { MSISENSOR_MSI } from '../../../../software/msisensor/msi/main.nf' addParams( options: [:] )
-
-workflow test_msisensor_msi {
-
-    def scaninput  = []
-    scaninput = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    scan = MSISENSOR_SCAN ( scaninput )
-
-    // IMPERFECT TEST:
-    // USING SARS-COV2 DATA AS NORMAL:TUMOR PAIR THIS WILL SUFFICE TO
-    // TEST MODULE EXECUTION, BUT NOT FUNCTIONALITY.
-    // FUNCTIONALITY HAS BEEN TESTED MANUALY USING AUTHOR-PROVIDED TEST
-    // DATA (https://github.com/ding-lab/msisensor/tree/master/test)
-    def input      = []
-
-    input = Channel.from([ [ id:'test', single_end:false ], // meta map
-               file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'],     checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'],         checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'],     checkIfExists: true) ])
-    //scan.txt.view()
-    input.concat(scan.txt).collect().view()
-    // BIT CLUMSY:
-    MSISENSOR_MSI ( input.concat(scan.txt).collect() )
-}

tests/software/msisensor/msi/test.yml

@@ -1,14 +0,0 @@
-- name: msisensor msi
-  command: nextflow run ./tests/software/msisensor/msi -entry test_msisensor_msi -c tests/config/nextflow.config
-  tags:
-    - msisensor
-    - msisensor_msi
-  files:
-    - path: output/msisensor/test
-      md5sum: a3290f7539dbbf83777e8590156c0e28
-    - path: output/msisensor/test_dis
-      md5sum: 060a3fc3701f3b10f6b19da9b21a32b7
-    - path: output/msisensor/test_germline
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/msisensor/test_somatic
-      md5sum: d41d8cd98f00b204e9800998ecf8427e

tests/software/msisensor/scan/main.nf

@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR_SCAN } from '../../../../software/msisensor/scan/main.nf' addParams( options: [:] )
-
-workflow test_msisensor_scan {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-
-    MSISENSOR_SCAN ( input )
-}

tests/software/msisensor/scan/test.yml

@@ -1,8 +0,0 @@
-- name: msisensor scan
-  command: nextflow run ./tests/software/msisensor/scan -entry test_msisensor_scan -c tests/config/nextflow.config
-  tags:
-    - msisensor
-    - msisensor_scan
-  files:
-    - path: output/msisensor/test.msisensor_scan.tab
-      md5sum: b7ae85acdcfc1a51e867ab3446d6fb59