-
Notifications
You must be signed in to change notification settings - Fork 428
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add: MSIsensor to Pair Somatic Variant Calling
- Loading branch information
Showing
10 changed files
with
132 additions
and
72 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| include { initOptions; saveFiles; getSoftwareName } from './../functions' | ||
|
|
||
| params.options = [:] | ||
| def options = initOptions(params.options) | ||
|
|
||
| environment = params.enable_conda ? "bioconda::msisensor=0.5" : null | ||
| container = "quay.io/biocontainers/msisensor:0.5--hb3646a4_2" | ||
| if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) container = "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2" | ||
|
|
||
| process MSISENSOR_MSI { | ||
| tag "${meta.id}" | ||
|
|
||
| label 'CPUS_1' | ||
| label 'MEMORY_MAX' | ||
|
|
||
| publishDir params.outdir, mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } | ||
|
|
||
| conda environment | ||
| container container | ||
|
|
||
| input: | ||
| tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor) | ||
| path msisensor_scan | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.list") | ||
|
|
||
| script: | ||
| def software = getSoftwareName(task.process) | ||
| def ioptions = initOptions(options) | ||
| def prefix = ioptions.suffix ? "msisensor_${meta.id}${ioptions.suffix}" : "msisensor_${meta.id}" | ||
| // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable | ||
| // 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" | ||
| """ | ||
| msisensor msi -d ${msisensor_scan} \ | ||
| -b 4 \ | ||
| -t ${bam_tumor} \ | ||
| -n ${bam_normal} \ | ||
| -o ${prefix} | ||
| mv ${prefix} ${prefix}.list | ||
| mv ${prefix}_dis ${prefix}_dis.list | ||
| mv ${prefix}_germline ${prefix}_germline.list | ||
| mv ${prefix}_somatic ${prefix}_somatic.list | ||
| """ | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| include { initOptions; saveFiles; getSoftwareName } from './../functions' | ||
|
|
||
| params.options = [:] | ||
| def options = initOptions(params.options) | ||
|
|
||
| environment = params.enable_conda ? "bioconda::msisensor=0.5" : null | ||
| container = "quay.io/biocontainers/msisensor:0.5--hb3646a4_2" | ||
| if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) container = "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2" | ||
|
|
||
| process MSISENSOR_SCAN { | ||
| tag "${fasta}" | ||
|
|
||
| label 'CPUS_1' | ||
| label 'MEMORY_MAX' | ||
|
|
||
| publishDir params.outdir, mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:"false") } | ||
|
|
||
| conda environment | ||
| container container | ||
|
|
||
| input: | ||
| path fasta | ||
| path fai | ||
|
|
||
| output: | ||
| path "microsatellites.list" | ||
|
|
||
| script: | ||
| def software = getSoftwareName(task.process) | ||
| def ioptions = initOptions(options) | ||
| def prefix = ioptions.suffix ? "msisensor_${ioptions.suffix}" : "msisensor_" | ||
| // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable | ||
| // 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" | ||
| """ | ||
| msisensor scan -d ${fasta} -o microsatellites.list | ||
| """ | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters