From 97ef01db1f342d3f7e800f14048ff4b0579967bf Mon Sep 17 00:00:00 2001 From: jemten Date: Mon, 10 Jun 2024 16:06:15 +0200 Subject: [PATCH 1/3] updates the default args for gens --- CHANGELOG.md | 1 + conf/modules/gens_pon.config | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bacac6a..733f7cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ Initial release of nf-core/createpanelrefs, created with the [nf-core](https://n - [#19](https://github.com/nf-core/createpanelrefs/pull/19) - Updates germlinecnvcaller subworkflow to handle exome samples - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals. +- [#28](https://github.com/nf-core/createpanelrefs/pull/28) - Updates default args for gens subworkflow ### `Fixed` diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config index 5ea92b5..e4ed2cc 100644 --- a/conf/modules/gens_pon.config +++ b/conf/modules/gens_pon.config @@ -52,8 +52,8 @@ process { } withName: '.*GENS_PON:GATK4_CREATEREADCOUNTPANELOFNORMALS' { - ext.args = { ["--minimum-interval-median-percentile 10.0", - "--maximum-chunk-size 29349635"].join(" ")} + ext.args = { ["--minimum-interval-median-percentile 5.0", + "--maximum-chunk-size 167772150"].join(" ")} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/gens_pon/createreadcountpanelofnormals" }, From 0bfcd5923906d4cb70355508078792804dca0d4d Mon Sep 17 00:00:00 2001 From: jemten Date: Tue, 11 Jun 2024 17:12:31 +0200 Subject: [PATCH 2/3] exposed gens args --- CHANGELOG.md | 2 +- conf/modules/gens_pon.config | 4 ++-- nextflow.config | 8 +++++--- nextflow_schema.json | 11 +++++++++++ 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 733f7cc..5f7ba4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ Initial release of nf-core/createpanelrefs, created with the [nf-core](https://n - [#19](https://github.com/nf-core/createpanelrefs/pull/19) - Updates germlinecnvcaller subworkflow to handle exome samples - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals. -- [#28](https://github.com/nf-core/createpanelrefs/pull/28) - Updates default args for gens subworkflow +- [#28](https://github.com/nf-core/createpanelrefs/pull/28) - Updates default args for gens subworkflow and made the parameters available from the command line. ### `Fixed` diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config index e4ed2cc..734d754 100644 --- a/conf/modules/gens_pon.config +++ b/conf/modules/gens_pon.config @@ -52,8 +52,8 @@ process { } withName: '.*GENS_PON:GATK4_CREATEREADCOUNTPANELOFNORMALS' { - ext.args = { ["--minimum-interval-median-percentile 5.0", - "--maximum-chunk-size 167772150"].join(" ")} + ext.args = { ["--minimum-interval-median-percentile ${params.gens_min_interval_median_percentile}", + "--maximum-chunk-size ${params.maximum_chunk_size}"].join(" ")} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/gens_pon/createreadcountpanelofnormals" }, diff --git a/nextflow.config b/nextflow.config index 67fee20..48eed54 100644 --- a/nextflow.config +++ b/nextflow.config @@ -32,9 +32,11 @@ params { gcnv_scatter_content = 5000 // Gens options - gens_bin_length = 100 - gens_pon_name = 'gens' - gens_readcount_format = 'HDF5' + gens_bin_length = 100 + gens_maximum_chunk_size = 167772150 + gens_min_interval_median_percentile = 5.0 + gens_pon_name = 'gens' + gens_readcount_format = 'HDF5' // CNVkit options cnvkit_targets = null diff --git a/nextflow_schema.json b/nextflow_schema.json index e05b538..36974d7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -127,6 +127,17 @@ "fa_icon": "fas fa-sort-numeric-down", "help_text": "Used by GATK's PreprocessIntervals. We recommend a bin length of 100." }, + "gens_maximum_chunk_size": { + "type": "number", + "default": 167772150, + "description": "Maximum chunk size when writing the HDF5 file" + }, + "gens_min_interval_median_percentile": { + "type": "number", + "default": 5, + "description": "Minimum interval median percentile for gatk CreateReadCountPanelOfNormals", + "help_text": "Genomic intervals with a median (across samples) of fractional coverage (optionally corrected for GC bias) less than or equal to this percentile are filtered out. (This is the first filter applied.)" + }, "gens_pon_name": { "type": "string", "description": "Name for panel of normals.", From d05b1fe78f21296ec2d8b87a49e5277ebfffa898 Mon Sep 17 00:00:00 2001 From: jemten Date: Tue, 11 Jun 2024 17:26:19 +0200 Subject: [PATCH 3/3] fix typo --- conf/modules/gens_pon.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config index 734d754..8ebd6cb 100644 --- a/conf/modules/gens_pon.config +++ b/conf/modules/gens_pon.config @@ -53,7 +53,7 @@ process { withName: '.*GENS_PON:GATK4_CREATEREADCOUNTPANELOFNORMALS' { ext.args = { ["--minimum-interval-median-percentile ${params.gens_min_interval_median_percentile}", - "--maximum-chunk-size ${params.maximum_chunk_size}"].join(" ")} + "--maximum-chunk-size ${params.gens_maximum_chunk_size}"].join(" ")} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/gens_pon/createreadcountpanelofnormals" },