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Code Issues Releases Packages Activity

Added kallistobustools/count (#409)

Browse source 
* Basic kb-python count functionality for scRNA-seq quantification working.

* Added tests and test data for workflow kite.

* Removed trailing whitespace

* Changed output channels to tuples with meta

Based on suggestions by @KevinMenden.

* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.

* Update software/kallistobustools/count/main.nf

@KevinMenden fixed wrong path definition

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Increased version of kb-python

* Updated tests with raw links.

* Fixed subtool referencing: kallistobustools/count

* Added newline

* Update software/kallistobustools/count/main.nf

Co-authored-by: Kevin Menden <kevin.menden@live.com>
This commit is contained in:
Florian Wuennemann 2021-04-30 01:27:17 -04:00 committed by GitHub
parent 6a31737cb8
commit 88dda738ac
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60
software/kallistobustools/count/functions.nf Normal file
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/*
* -----------------------------------------------------
* 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"
}
}
}

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process KALLISTOBUSTOOLS_COUNT {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
}
input:
tuple val(meta), path(reads)
path index
path t2g
path t1c
path t2c
val use_t1c
val use_t2c
val workflow
val technology
output:
tuple val(meta), path ("*_kallistobustools_count") , emit: kallistobustools_count
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def cdna = use_t1c ? "-c1 $t1c" : ''
def introns = use_t2c ? "-c2 $t2c" : ''
"""
kb \\
count \\
-t $task.cpus \\
-i $index \\
-g $t2g \\
$cdna \\
$introns \\
--workflow $workflow \\
-x $technology \\
$options.args \\
-o ${prefix}_kallistobustools_count \\
${reads[0]} \\
${reads[1]}
echo \$(kb 2>&1) | sed 's/^kb_python //; s/Usage.*\$//' > ${software}.version.txt
"""
}

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name: kallistobustools_count
description: quantifies scRNA-seq data from fastq files using kb-python.
keywords:
- scRNA-seq
- count
tools:
- kb:
description: kallisto and bustools are wrapped in an easy-to-use program called kb
homepage: https://www.kallistobus.tools/
documentation: https://kb-python.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/pachterlab/kb_python
doi: ""
licence: MIT License
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastq1:
type: file
description: Read 1 fastq file
pattern: "*.{fastq,fastq.gz}"
- fastq2:
type: file
description: Read 2 fastq file
pattern: "*.{fastq,fastq.gz}"
- index:
type: file
description: kb-ref index file (.idx)
pattern: "*.{idx}"
- t2g:
type: file
description: t2g file from kallisto
pattern: "*t2g.txt"
- t1c:
type: file
description: kb ref's c1 spliced_t2c file
pattern: "*.{cdna_t2c.txt}"
- use_t1c:
type: boolean
description: Whether to use the c1 txt file for RNA velocity and nucleus workflows
- t2c:
type: file
description: kb ref's c2 unspliced_t2c file
pattern: "*.{introns_t2c.txt}"
- use_t2c:
type: boolean
description: Whether to use the c2 txt file for RNA velocity and nucleus workflows
- kb_workflow:
type: value
description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
pattern: "{standard,lamanno,nucleus,kite}"
- technology:
type: value
description: String value defining the sequencing technology used.
pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- kallistobustools_count:
type: file
description: kb count output folder
pattern: "*_{kallistobustools_count}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@flowuenne"

4
tests/config/pytest_software.yml
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- software/kallisto/index/**
- tests/software/kallisto/index/**
kallistobustools/count:
- software/kallistobustools/count/**
- tests/software/kallistobustools/count/**
kallistobustools/ref:
- software/kallistobustools/ref/**
- tests/software/kallistobustools/ref/**

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CD45RA-0.3 CD45RA CD45RA
CD45RA-1.1 CD45RA CD45RA
CD45RA-1.2 CD45RA CD45RA
CD45RA-1.3 CD45RA CD45RA
CD45RA-2.1 CD45RA CD45RA
CD45RA-2.2 CD45RA CD45RA
CD45RA-2.3 CD45RA CD45RA
CD45RA-3.1 CD45RA CD45RA
CD45RA-3.2 CD45RA CD45RA
CD45RA-3.3 CD45RA CD45RA
CD45RA-4.1 CD45RA CD45RA
CD45RA-4.2 CD45RA CD45RA
CD45RA-4.3 CD45RA CD45RA
CD45RA-5.1 CD45RA CD45RA
CD45RA-5.2 CD45RA CD45RA
CD45RA-5.3 CD45RA CD45RA
CD45RA-6.1 CD45RA CD45RA
CD45RA-6.2 CD45RA CD45RA
CD45RA-6.3 CD45RA CD45RA
CD45RA-7.1 CD45RA CD45RA
CD45RA-7.2 CD45RA CD45RA
CD45RA-7.3 CD45RA CD45RA
CD45RA-8.1 CD45RA CD45RA
CD45RA-8.2 CD45RA CD45RA
CD45RA-8.3 CD45RA CD45RA
CD45RA-9.1 CD45RA CD45RA
CD45RA-9.2 CD45RA CD45RA
CD45RA-9.3 CD45RA CD45RA
CD45RA-10.1 CD45RA CD45RA
CD45RA-10.2 CD45RA CD45RA
CD45RA-10.3 CD45RA CD45RA
CD45RA-11.1 CD45RA CD45RA
CD45RA-11.2 CD45RA CD45RA
CD45RA-11.3 CD45RA CD45RA
CD45RA-12.1 CD45RA CD45RA
CD45RA-12.2 CD45RA CD45RA
CD45RA-12.3 CD45RA CD45RA
CD45RA-13.1 CD45RA CD45RA
CD45RA-13.2 CD45RA CD45RA
CD45RA-13.3 CD45RA CD45RA
CD45RA-14.1 CD45RA CD45RA
CD45RA-14.2 CD45RA CD45RA
CD45RA-14.3 CD45RA CD45RA
CD45RO CD45RO CD45RO
CD45RO-0.1 CD45RO CD45RO
CD45RO-0.2 CD45RO CD45RO
CD45RO-0.3 CD45RO CD45RO
CD45RO-1.1 CD45RO CD45RO
CD45RO-1.2 CD45RO CD45RO
CD45RO-1.3 CD45RO CD45RO
CD45RO-2.1 CD45RO CD45RO
CD45RO-2.2 CD45RO CD45RO
CD45RO-2.3 CD45RO CD45RO
CD45RO-3.1 CD45RO CD45RO
CD45RO-3.2 CD45RO CD45RO
CD45RO-3.3 CD45RO CD45RO
CD45RO-4.1 CD45RO CD45RO
CD45RO-4.2 CD45RO CD45RO
CD45RO-4.3 CD45RO CD45RO
CD45RO-5.1 CD45RO CD45RO
CD45RO-5.2 CD45RO CD45RO
CD45RO-5.3 CD45RO CD45RO
CD45RO-6.1 CD45RO CD45RO
CD45RO-6.2 CD45RO CD45RO
CD45RO-6.3 CD45RO CD45RO
CD45RO-7.1 CD45RO CD45RO
CD45RO-7.2 CD45RO CD45RO
CD45RO-7.3 CD45RO CD45RO
CD45RO-8.1 CD45RO CD45RO
CD45RO-8.2 CD45RO CD45RO
CD45RO-8.3 CD45RO CD45RO
CD45RO-9.1 CD45RO CD45RO
CD45RO-9.2 CD45RO CD45RO
CD45RO-9.3 CD45RO CD45RO
CD45RO-10.1 CD45RO CD45RO
CD45RO-10.2 CD45RO CD45RO
CD45RO-10.3 CD45RO CD45RO
CD45RO-11.1 CD45RO CD45RO
CD45RO-11.2 CD45RO CD45RO
CD45RO-11.3 CD45RO CD45RO
CD45RO-12.1 CD45RO CD45RO
CD45RO-12.2 CD45RO CD45RO
CD45RO-12.3 CD45RO CD45RO
CD45RO-13.1 CD45RO CD45RO
CD45RO-13.2 CD45RO CD45RO
CD45RO-13.3 CD45RO CD45RO
CD45RO-14.1 CD45RO CD45RO
CD45RO-14.2 CD45RO CD45RO
CD45RO-14.3 CD45RO CD45RO
PD-1 PD-1 PD-1
PD-1-0.1 PD-1 PD-1
PD-1-0.2 PD-1 PD-1
PD-1-0.3 PD-1 PD-1
PD-1-1.1 PD-1 PD-1
PD-1-1.2 PD-1 PD-1
PD-1-1.3 PD-1 PD-1
PD-1-2.1 PD-1 PD-1
PD-1-2.2 PD-1 PD-1
PD-1-2.3 PD-1 PD-1
PD-1-3.1 PD-1 PD-1
PD-1-3.2 PD-1 PD-1
PD-1-3.3 PD-1 PD-1
PD-1-4.1 PD-1 PD-1
PD-1-4.2 PD-1 PD-1
PD-1-4.3 PD-1 PD-1
PD-1-5.1 PD-1 PD-1
PD-1-5.2 PD-1 PD-1
PD-1-5.3 PD-1 PD-1
PD-1-6.1 PD-1 PD-1
PD-1-6.2 PD-1 PD-1
PD-1-6.3 PD-1 PD-1
PD-1-7.1 PD-1 PD-1
PD-1-7.2 PD-1 PD-1
PD-1-7.3 PD-1 PD-1
PD-1-8.1 PD-1 PD-1
PD-1-8.2 PD-1 PD-1
PD-1-8.3 PD-1 PD-1
PD-1-9.1 PD-1 PD-1
PD-1-9.2 PD-1 PD-1
PD-1-9.3 PD-1 PD-1
PD-1-10.1 PD-1 PD-1
PD-1-10.2 PD-1 PD-1
PD-1-10.3 PD-1 PD-1
PD-1-11.1 PD-1 PD-1
PD-1-11.2 PD-1 PD-1
PD-1-11.3 PD-1 PD-1
PD-1-12.1 PD-1 PD-1
PD-1-12.2 PD-1 PD-1
PD-1-12.3 PD-1 PD-1
PD-1-13.1 PD-1 PD-1
PD-1-13.2 PD-1 PD-1
PD-1-13.3 PD-1 PD-1
PD-1-14.1 PD-1 PD-1
PD-1-14.2 PD-1 PD-1
PD-1-14.3 PD-1 PD-1
TIGIT TIGIT TIGIT
TIGIT-0.1 TIGIT TIGIT
TIGIT-0.2 TIGIT TIGIT
TIGIT-0.3 TIGIT TIGIT
TIGIT-1.1 TIGIT TIGIT
TIGIT-1.2 TIGIT TIGIT
TIGIT-1.3 TIGIT TIGIT
TIGIT-2.1 TIGIT TIGIT
TIGIT-2.2 TIGIT TIGIT
TIGIT-2.3 TIGIT TIGIT
TIGIT-3.1 TIGIT TIGIT
TIGIT-3.2 TIGIT TIGIT
TIGIT-3.3 TIGIT TIGIT
TIGIT-4.1 TIGIT TIGIT
TIGIT-4.2 TIGIT TIGIT
TIGIT-4.3 TIGIT TIGIT
TIGIT-5.1 TIGIT TIGIT
TIGIT-5.2 TIGIT TIGIT
TIGIT-5.3 TIGIT TIGIT
TIGIT-6.1 TIGIT TIGIT
TIGIT-6.2 TIGIT TIGIT
TIGIT-6.3 TIGIT TIGIT
TIGIT-7.1 TIGIT TIGIT
TIGIT-7.2 TIGIT TIGIT
TIGIT-7.3 TIGIT TIGIT
TIGIT-8.1 TIGIT TIGIT
TIGIT-8.2 TIGIT TIGIT
TIGIT-8.3 TIGIT TIGIT
TIGIT-9.1 TIGIT TIGIT
TIGIT-9.2 TIGIT TIGIT
TIGIT-9.3 TIGIT TIGIT
TIGIT-10.1 TIGIT TIGIT
TIGIT-10.2 TIGIT TIGIT
TIGIT-10.3 TIGIT TIGIT
TIGIT-11.1 TIGIT TIGIT
TIGIT-11.2 TIGIT TIGIT
TIGIT-11.3 TIGIT TIGIT
TIGIT-12.1 TIGIT TIGIT
TIGIT-12.2 TIGIT TIGIT
TIGIT-12.3 TIGIT TIGIT
TIGIT-13.1 TIGIT TIGIT
TIGIT-13.2 TIGIT TIGIT
TIGIT-13.3 TIGIT TIGIT
TIGIT-14.1 TIGIT TIGIT
TIGIT-14.2 TIGIT TIGIT
TIGIT-14.3 TIGIT TIGIT
CD127 CD127 CD127
CD127-0.1 CD127 CD127
CD127-0.2 CD127 CD127
CD127-0.3 CD127 CD127
CD127-1.1 CD127 CD127
CD127-1.2 CD127 CD127
CD127-1.3 CD127 CD127
CD127-2.1 CD127 CD127
CD127-2.2 CD127 CD127
CD127-2.3 CD127 CD127
CD127-3.1 CD127 CD127
CD127-3.2 CD127 CD127
CD127-3.3 CD127 CD127
CD127-4.1 CD127 CD127
CD127-4.2 CD127 CD127
CD127-4.3 CD127 CD127
CD127-5.1 CD127 CD127
CD127-5.2 CD127 CD127
CD127-5.3 CD127 CD127
CD127-6.1 CD127 CD127
CD127-6.2 CD127 CD127
CD127-6.3 CD127 CD127
CD127-7.1 CD127 CD127
CD127-7.2 CD127 CD127
CD127-7.3 CD127 CD127
CD127-8.1 CD127 CD127
CD127-8.2 CD127 CD127
CD127-8.3 CD127 CD127
CD127-9.1 CD127 CD127
CD127-9.2 CD127 CD127
CD127-9.3 CD127 CD127
CD127-10.1 CD127 CD127
CD127-10.2 CD127 CD127
CD127-10.3 CD127 CD127
CD127-11.1 CD127 CD127
CD127-11.2 CD127 CD127
CD127-11.3 CD127 CD127
CD127-12.1 CD127 CD127
CD127-12.2 CD127 CD127
CD127-12.3 CD127 CD127
CD127-13.1 CD127 CD127
CD127-13.2 CD127 CD127
CD127-13.3 CD127 CD127
CD127-14.1 CD127 CD127
CD127-14.2 CD127 CD127
CD127-14.3 CD127 CD127
IgG2a IgG2a IgG2a
IgG2a-0.1 IgG2a IgG2a
IgG2a-0.2 IgG2a IgG2a
IgG2a-0.3 IgG2a IgG2a
IgG2a-1.1 IgG2a IgG2a
IgG2a-1.2 IgG2a IgG2a
IgG2a-1.3 IgG2a IgG2a
IgG2a-2.1 IgG2a IgG2a
IgG2a-2.2 IgG2a IgG2a
IgG2a-2.3 IgG2a IgG2a
IgG2a-3.1 IgG2a IgG2a
IgG2a-3.2 IgG2a IgG2a
IgG2a-3.3 IgG2a IgG2a
IgG2a-4.1 IgG2a IgG2a
IgG2a-4.2 IgG2a IgG2a
IgG2a-4.3 IgG2a IgG2a
IgG2a-5.1 IgG2a IgG2a
IgG2a-5.2 IgG2a IgG2a
IgG2a-5.3 IgG2a IgG2a
IgG2a-6.1 IgG2a IgG2a
IgG2a-6.2 IgG2a IgG2a
IgG2a-6.3 IgG2a IgG2a
IgG2a-7.1 IgG2a IgG2a
IgG2a-7.2 IgG2a IgG2a
IgG2a-7.3 IgG2a IgG2a
IgG2a-8.1 IgG2a IgG2a
IgG2a-8.2 IgG2a IgG2a
IgG2a-8.3 IgG2a IgG2a
IgG2a-9.1 IgG2a IgG2a
IgG2a-9.2 IgG2a IgG2a
IgG2a-9.3 IgG2a IgG2a
IgG2a-10.1 IgG2a IgG2a
IgG2a-10.2 IgG2a IgG2a
IgG2a-10.3 IgG2a IgG2a
IgG2a-11.1 IgG2a IgG2a
IgG2a-11.2 IgG2a IgG2a
IgG2a-11.3 IgG2a IgG2a
IgG2a-12.1 IgG2a IgG2a
IgG2a-12.2 IgG2a IgG2a
IgG2a-12.3 IgG2a IgG2a
IgG2a-13.1 IgG2a IgG2a
IgG2a-13.2 IgG2a IgG2a
IgG2a-13.3 IgG2a IgG2a
IgG2a-14.1 IgG2a IgG2a
IgG2a-14.2 IgG2a IgG2a
IgG2a-14.3 IgG2a IgG2a
IgG1 IgG1 IgG1
IgG1-0.1 IgG1 IgG1
IgG1-0.2 IgG1 IgG1
IgG1-0.3 IgG1 IgG1
IgG1-1.1 IgG1 IgG1
IgG1-1.2 IgG1 IgG1
IgG1-1.3 IgG1 IgG1
IgG1-2.1 IgG1 IgG1
IgG1-2.2 IgG1 IgG1
IgG1-2.3 IgG1 IgG1
IgG1-3.1 IgG1 IgG1
IgG1-3.2 IgG1 IgG1
IgG1-3.3 IgG1 IgG1
IgG1-4.1 IgG1 IgG1
IgG1-4.2 IgG1 IgG1
IgG1-4.3 IgG1 IgG1
IgG1-5.1 IgG1 IgG1
IgG1-5.2 IgG1 IgG1
IgG1-5.3 IgG1 IgG1
IgG1-6.1 IgG1 IgG1
IgG1-6.2 IgG1 IgG1
IgG1-6.3 IgG1 IgG1
IgG1-7.1 IgG1 IgG1
IgG1-7.2 IgG1 IgG1
IgG1-7.3 IgG1 IgG1
IgG1-8.1 IgG1 IgG1
IgG1-8.2 IgG1 IgG1
IgG1-8.3 IgG1 IgG1
IgG1-9.1 IgG1 IgG1
IgG1-9.2 IgG1 IgG1
IgG1-9.3 IgG1 IgG1
IgG1-10.1 IgG1 IgG1
IgG1-10.2 IgG1 IgG1
IgG1-10.3 IgG1 IgG1
IgG1-11.1 IgG1 IgG1
IgG1-11.2 IgG1 IgG1
IgG1-11.3 IgG1 IgG1
IgG1-12.1 IgG1 IgG1
IgG1-12.2 IgG1 IgG1
IgG1-12.3 IgG1 IgG1
IgG1-13.1 IgG1 IgG1
IgG1-13.2 IgG1 IgG1
IgG1-13.3 IgG1 IgG1
IgG1-14.1 IgG1 IgG1
IgG1-14.2 IgG1 IgG1
IgG1-14.3 IgG1 IgG1
IgG2b IgG2b IgG2b
IgG2b-0.1 IgG2b IgG2b
IgG2b-0.2 IgG2b IgG2b
IgG2b-0.3 IgG2b IgG2b
IgG2b-1.1 IgG2b IgG2b
IgG2b-1.2 IgG2b IgG2b
IgG2b-1.3 IgG2b IgG2b
IgG2b-2.1 IgG2b IgG2b
IgG2b-2.2 IgG2b IgG2b
IgG2b-2.3 IgG2b IgG2b
IgG2b-3.1 IgG2b IgG2b
IgG2b-3.2 IgG2b IgG2b
IgG2b-3.3 IgG2b IgG2b
IgG2b-4.1 IgG2b IgG2b
IgG2b-4.2 IgG2b IgG2b
IgG2b-4.3 IgG2b IgG2b
IgG2b-5.1 IgG2b IgG2b
IgG2b-5.2 IgG2b IgG2b
IgG2b-5.3 IgG2b IgG2b
IgG2b-6.1 IgG2b IgG2b
IgG2b-6.2 IgG2b IgG2b
IgG2b-6.3 IgG2b IgG2b
IgG2b-7.1 IgG2b IgG2b
IgG2b-7.2 IgG2b IgG2b
IgG2b-7.3 IgG2b IgG2b
IgG2b-8.1 IgG2b IgG2b
IgG2b-8.2 IgG2b IgG2b
IgG2b-8.3 IgG2b IgG2b
IgG2b-9.1 IgG2b IgG2b
IgG2b-9.2 IgG2b IgG2b
IgG2b-9.3 IgG2b IgG2b
IgG2b-10.1 IgG2b IgG2b
IgG2b-10.2 IgG2b IgG2b
IgG2b-10.3 IgG2b IgG2b
IgG2b-11.1 IgG2b IgG2b
IgG2b-11.2 IgG2b IgG2b
IgG2b-11.3 IgG2b IgG2b
IgG2b-12.1 IgG2b IgG2b
IgG2b-12.2 IgG2b IgG2b
IgG2b-12.3 IgG2b IgG2b
IgG2b-13.1 IgG2b IgG2b
IgG2b-13.2 IgG2b IgG2b
IgG2b-13.3 IgG2b IgG2b
IgG2b-14.1 IgG2b IgG2b
IgG2b-14.2 IgG2b IgG2b
IgG2b-14.3 IgG2b IgG2b

46
tests/data/delete_me/kallistobustools/count/t2g.txt Normal file
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ENSMUST00000237047.2 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-209 chr19 3103071 3247732 -
ENSMUST00000236704.2 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-208 chr19 3115711 3247714 -
ENSMUST00000190575.7 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-203 chr19 3115711 3247714 -
ENSMUST00000235916.2 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-207 chr19 3195868 3247716 -
ENSMUST00000189643.2 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-201 chr19 3195870 3210190 -
ENSMUST00000191405.7 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-206 chr19 3195946 3210181 -
ENSMUST00000190668.7 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-204 chr19 3199813 3247698 -
ENSMUST00000190982.7 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-205 chr19 3203208 3247698 -
ENSMUST00000190259.2 ENSMUSG00000100969.8 1700030N03Rik 1700030N03Rik-202 chr19 3203799 3247703 -
ENSMUST00000235610.2 ENSMUSG00000117761.2 Gm50428 Gm50428-201 chr19 3184645 3184959 +
ENSMUST00000101978.3 ENSMUSG00000118966.1 AC162463.2 AC162463.2-201 chr19 3186984 3187090 -
ENSMUST00000235785.2 ENSMUSG00000118182.2 Gm50427 Gm50427-201 chr19 3192760 3193065 +
ENSMUST00000237449.2 ENSMUSG00000117928.2 Gm42068 Gm42068-201 chr19 3206623 3207012 +
ENSMUST00000240363.1 ENSMUSG00000118771.1 AC162463.1 AC162463.1-201 chr19 3207710 3207835 -
ENSMUST00000236616.2 ENSMUSG00000118393.2 Gm50426 Gm50426-201 chr19 3234959 3235273 +
ENSMUST00000236294.2 ENSMUSG00000118052.2 Gm50432 Gm50432-202 chr19 3255607 3256258 +
ENSMUST00000235308.2 ENSMUSG00000118052.2 Gm50432 Gm50432-201 chr19 3255793 3256070 +
ENSMUST00000236416.2 ENSMUSG00000118203.2 Gm7798 Gm7798-201 chr19 3298804 3300214 +
ENSMUST00000237524.2 ENSMUSG00000117886.2 Gm2106 Gm2106-201 chr19 3303518 3305067 -
ENSMUST00000025751.11 ENSMUSG00000024831.15 Ighmbp2 Ighmbp2-201 chr19 3309076 3333017 -
ENSMUST00000119292.8 ENSMUSG00000024831.15 Ighmbp2 Ighmbp2-202 chr19 3310924 3332979 -
ENSMUST00000154537.8 ENSMUSG00000024831.15 Ighmbp2 Ighmbp2-204 chr19 3314818 3332980 -
ENSMUST00000143079.2 ENSMUSG00000024831.15 Ighmbp2 Ighmbp2-203 chr19 3315364 3317716 -
ENSMUST00000025745.10 ENSMUSG00000024829.13 Mrpl21 Mrpl21-202 chr19 3332901 3342837 +
ENSMUST00000139844.8 ENSMUSG00000024829.13 Mrpl21 Mrpl21-203 chr19 3333055 3339179 +
ENSMUST00000155870.2 ENSMUSG00000024829.13 Mrpl21 Mrpl21-206 chr19 3333060 3335325 +
ENSMUST00000025743.7 ENSMUSG00000024829.13 Mrpl21 Mrpl21-201 chr19 3333060 3341201 +
ENSMUST00000141610.2 ENSMUSG00000024829.13 Mrpl21 Mrpl21-204 chr19 3333064 3337739 +
ENSMUST00000154785.2 ENSMUSG00000024829.13 Mrpl21 Mrpl21-205 chr19 3336811 3341195 +
ENSMUST00000185105.3 ENSMUSG00000099261.3 Mir6984 Mir6984-201 chr19 3338920 3338983 +
ENSMUST00000237542.2 ENSMUSG00000118213.2 Gm50307 Gm50307-201 chr19 3366782 3367581 -
ENSMUST00000237938.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-206 chr19 3372334 3420748 +
ENSMUST00000025835.6 ENSMUSG00000024900.6 Cpt1a Cpt1a-201 chr19 3373285 3435733 +
ENSMUST00000235968.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-202 chr19 3373348 3401674 +
ENSMUST00000237562.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-205 chr19 3383725 3408277 +
ENSMUST00000238015.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-207 chr19 3391627 3414538 +
ENSMUST00000237457.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-204 chr19 3416330 3419217 +
ENSMUST00000237444.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-203 chr19 3425040 3428498 +
ENSMUST00000238027.2 ENSMUSG00000024900.6 Cpt1a Cpt1a-208 chr19 3426344 3433866 +
ENSMUST00000025840.16 ENSMUSG00000024905.16 Tesmin Tesmin-201 chr19 3438857 3457823 +
ENSMUST00000151341.8 ENSMUSG00000024905.16 Tesmin Tesmin-204 chr19 3438885 3448172 +
ENSMUST00000127142.2 ENSMUSG00000024905.16 Tesmin Tesmin-202 chr19 3439379 3457289 +
ENSMUST00000142193.8 ENSMUSG00000024905.16 Tesmin Tesmin-203 chr19 3439379 3457785 +
ENSMUST00000237521.2 ENSMUSG00000024907.8 Gal Gal-202 chr19 3459915 3464544 -
ENSMUST00000025842.8 ENSMUSG00000024907.8 Gal Gal-201 chr19 3459932 3464447 -
ENSMUST00000025846.16 ENSMUSG00000024908.16 Ppp6r3 Ppp6r3-201 chr19 3504928 3625720 -

24
tests/software/kallistobustools/count/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { KALLISTOBUSTOOLS_COUNT } from '../../../../software/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
workflow test_kallistobustools_count {
input = [ [id:'test_standard'], // meta map
[file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_1.fastq.gz?raw=true", checkIfExists: true),
file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_2.fastq.gz?raw=true", checkIfExists: true)]
]
index = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
t2g = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
t1c = file('t1c_dummy')
t2c = file('t2c_dummy')
use_t1c = false
use_t2c = false
workflow = "standard"
technology = "10XV3"
KALLISTOBUSTOOLS_COUNT (input,index,t2g,t1c,t2c,use_t1c,use_t2c,workflow,technology)
}

36
tests/software/kallistobustools/count/test.yml Normal file
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- name: kallistobustools count test_kallistobustools_count
command: nextflow run tests/software/kallistobustools/count -entry test_kallistobustools_count -c tests/config/nextflow.config
tags:
- kallistobustools/count
- kallistobustools
files:
- path: output/kallistobustools/test_standard_kallistobustools_count/10xv3_whitelist.txt
md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/barcodes.tsv
md5sum: 8f734732c46f52c4d1c025bfe4134bd2
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/genes.tsv
md5sum: fbebf995a3de568db8ac028cd0c5d993
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/matrix.mtx
md5sum: 4847bae27c41961496d504bcfe9890ba
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.barcodes.txt
md5sum: cafdf96423987e3d9e807cdc16139541
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.genes.txt
md5sum: 52d0627aaf0418bebe3ef75ad77da53f
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.mtx
md5sum: d05e1582385ba5f215fa73c470343c06
- path: output/kallistobustools/test_standard_kallistobustools_count/inspect.json
md5sum: d3d23063f3fc07f7fbd24748aa4271a9
- path: output/kallistobustools/test_standard_kallistobustools_count/kb_info.json
contains:
- 'kallisto'
- path: output/kallistobustools/test_standard_kallistobustools_count/matrix.ec
md5sum: cd8340e3fb78d74ad85fabdbe0a778f0
- path: output/kallistobustools/test_standard_kallistobustools_count/output.bus
md5sum: f4702922bd0c142e34b3680c2251426a
- path: output/kallistobustools/test_standard_kallistobustools_count/output.unfiltered.bus
md5sum: e38f99748e598e33fe035b89e7c89fb5
- path: output/kallistobustools/test_standard_kallistobustools_count/run_info.json
contains:
- 'n_targets'
- path: output/kallistobustools/test_standard_kallistobustools_count/transcripts.txt
md5sum: 6d583083eaf6ca81e409332a40d2e74c