From e4e4f8090caa7c2f3fd71caa62792a1ea9ff4b59 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 May 2022 23:59:12 +0200 Subject: [PATCH 1/4] combine multiple pytor --- modules/cnvpytor/view/main.nf | 16 +++++++++------- tests/modules/cnvpytor/view/main.nf | 6 +++--- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/modules/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf index ad2249b8..1bb61a38 100644 --- a/modules/cnvpytor/view/main.nf +++ b/modules/cnvpytor/view/main.nf @@ -8,7 +8,7 @@ process CNVPYTOR_VIEW { 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" input: - tuple val(meta), path(pytor) + tuple val(meta), path(pytor_files) val bin_sizes val output_format @@ -23,17 +23,18 @@ process CNVPYTOR_VIEW { script: def output_suffix = output_format ?: 'vcf' - def bins = bin_sizes ?: '1000' + def bins = bin_sizes ?: '1000' + def input = pytor_files.join(" ") + def prefix = task.ext.prefix ?: "${meta.id}" """ python3 < versions.yml "${task.process}": diff --git a/tests/modules/cnvpytor/view/main.nf b/tests/modules/cnvpytor/view/main.nf index b865dd6d..3b99c314 100644 --- a/tests/modules/cnvpytor/view/main.nf +++ b/tests/modules/cnvpytor/view/main.nf @@ -8,7 +8,7 @@ workflow test_cnvpytor_view { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true) + [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)] ] bin_sizes = "10000 100000" @@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true) + [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)] ] output_suffix = "tsv" @@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true) + [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)] ] bin_sizes = [] From af73544010cc9563ec7d7160aeb825ae28ec217f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 May 2022 00:13:49 +0200 Subject: [PATCH 2/4] update meta --- modules/cnvpytor/view/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml index 1392e90e..e4e68fad 100644 --- a/modules/cnvpytor/view/meta.yml +++ b/modules/cnvpytor/view/meta.yml @@ -17,9 +17,9 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test' ] - - pytor: + - pytor_files: type: file - description: pytor file containing read depth data + description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files. pattern: "*.{pytor}" - bin_sizes: type: string From 313d76e00525c8e975dabce0c34973fd53c3f4dd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 May 2022 00:18:16 +0200 Subject: [PATCH 3/4] update svdb version --- modules/svdb/merge/main.nf | 6 +++--- modules/svdb/query/main.nf | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf index 4a39940c..0d56fea2 100644 --- a/modules/svdb/merge/main.nf +++ b/modules/svdb/merge/main.nf @@ -2,10 +2,10 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null) + conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0': - 'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }" + 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': + 'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }" input: tuple val(meta), path(vcfs) diff --git a/modules/svdb/query/main.nf b/modules/svdb/query/main.nf index c669b5a5..dbab5259 100644 --- a/modules/svdb/query/main.nf +++ b/modules/svdb/query/main.nf @@ -2,10 +2,10 @@ process SVDB_QUERY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null) + conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0': - 'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }" + 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': + 'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }" input: tuple val(meta), path(vcf) From 1ccea5ff4d3dffbf9a8e53032481cc9246d4e23d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 May 2022 10:56:58 +0200 Subject: [PATCH 4/4] remove prefix def in callcnvs --- modules/cnvpytor/callcnvs/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf index 092f6def..69c9d40e 100644 --- a/modules/cnvpytor/callcnvs/main.nf +++ b/modules/cnvpytor/callcnvs/main.nf @@ -20,7 +20,6 @@ process CNVPYTOR_CALLCNVS { script: def bins = bin_sizes ?: '1000' - def prefix = task.ext.prefix ?: "${meta.id}" """ cnvpytor \\ -root $pytor \\