diff --git a/modules/msk/phylowgs/multievolve/environment.yml b/modules/msk/phylowgs/multievolve/environment.yml index d6a0ba5e..2ccd979f 100644 --- a/modules/msk/phylowgs/multievolve/environment.yml +++ b/modules/msk/phylowgs/multievolve/environment.yml @@ -1,9 +1,6 @@ --- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "phylowgs_multievolve" channels: - conda-forge - bioconda - - defaults dependencies: - - "PHYLOWGS" + - "PHYLOWGS=NA" diff --git a/modules/msk/phylowgs/multievolve/main.nf b/modules/msk/phylowgs/multievolve/main.nf index d7f6e9c7..117c78d3 100644 --- a/modules/msk/phylowgs/multievolve/main.nf +++ b/modules/msk/phylowgs/multievolve/main.nf @@ -19,13 +19,11 @@ process PHYLOWGS_MULTIEVOLVE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def threads = task.cpus * 2 """ python2 \\ /usr/bin/multievolve.py \\ ${args} \\ - --num-chains ${threads} \\ --ssms ${ssm_data} \\ --cnvs ${cnv_data} diff --git a/modules/msk/phylowgs/multievolve/meta.yml b/modules/msk/phylowgs/multievolve/meta.yml index 0ccb999b..a1999dea 100644 --- a/modules/msk/phylowgs/multievolve/meta.yml +++ b/modules/msk/phylowgs/multievolve/meta.yml @@ -1,5 +1,4 @@ --- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "phylowgs_multievolve" description: Create trees from input from phylowgs_createinput keywords: @@ -13,34 +12,36 @@ tools: tool_dev_url: "https://github.com/mskcc/phylowgs" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - cnv_data: - type: file - description: copy number input data from phylowgs_createinput - pattern: "*.{txt}" - - ssm_data: - type: file - description: mutation input data from phylowgs_createinput - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - cnv_data: + type: file + description: copy number input data from phylowgs_createinput + pattern: "*.{txt}" + - ssm_data: + type: file + description: mutation input data from phylowgs_createinput + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - trees: - type: file - description: Zip file containing the completed trees - pattern: "trees.zip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - chains/trees.zip: + type: file + description: Zip file containing the completed trees + pattern: "trees.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nikhil" diff --git a/modules/msk/phylowgs/multievolve/tests/nextflow.config b/modules/msk/phylowgs/multievolve/tests/nextflow.config index 43986ff2..2af68890 100644 --- a/modules/msk/phylowgs/multievolve/tests/nextflow.config +++ b/modules/msk/phylowgs/multievolve/tests/nextflow.config @@ -5,6 +5,6 @@ params { process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: 'PHYLOWGS_MULTIEVOLVE' { - ext.args = '--burnin-samples 2 --mcmc-samples 2' + ext.args = '--num-chains 2 --burnin-samples 2 --mcmc-samples 2' } }