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

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This reverts commit fead37d57a.
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kevbrick 2021-03-25 16:46:31 -04:00 committed by GitHub
parent fead37d57a
commit c29ad052bd
11 changed files with 0 additions and 391 deletions
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60
software/msisensor/msi/functions.nf
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@ -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"
}
}
}

45
software/msisensor/msi/main.nf
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@ -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
"""
}

69
software/msisensor/msi/meta.yml
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@ -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"

60
software/msisensor/scan/functions.nf
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@ -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"
}
}
}

40
software/msisensor/scan/main.nf
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@ -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
"""
}

42
software/msisensor/scan/meta.yml
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@ -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"

8
tests/config/pytest_software.yml
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@ -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/**

31
tests/software/msisensor/msi/main.nf
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@ -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() )
}

14
tests/software/msisensor/msi/test.yml
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@ -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

14
tests/software/msisensor/scan/main.nf
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@ -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 )
}

8
tests/software/msisensor/scan/test.yml
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@ -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