From f738e5b9adef750e4ea3a224f987d1b9c75a9b56 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Sat, 29 Jul 2023 11:14:12 -0400 Subject: [PATCH] add skip report threshold --- nextflow.config | 1 + nextflow_schema.json | 5 +++++ subworkflows/local/clonal_analysis.nf | 15 ++++++++------- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/nextflow.config b/nextflow.config index 21647655..2b226b99 100644 --- a/nextflow.config +++ b/nextflow.config @@ -79,6 +79,7 @@ params { singlecell = 'single_cell' clonal_threshold = 'auto' skip_all_clones_report = false + skip_report_threshold = false // tree lineage options igphyml="/usr/local/bin/igphyml" diff --git a/nextflow_schema.json b/nextflow_schema.json index b05ac808..541fb42d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -364,6 +364,11 @@ "type": "boolean", "description": "Skip report of EnchantR DefineClones for all samples together.", "fa_icon": "fas fa-angle-double-right" + }, + "skip_report_threshold": { + "type": "boolean", + "description": "Skip report of EnchantR FindThreshold for all samples together.", + "fa_icon": "fas fa-angle-double-right" } }, "help_text": "By default, the pipeline will define clones for each of the samples, as two sequences having the same V-gene assignment, C-gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the CDR3 sequences will be assessed by Hamming distances. \n\nA distance threshold for determining if two sequences come from the same clone or not is automatically determined by the process find threshold. Alternatively, a hamming distance threshold can be manually set by setting the `--clonal_threshold` parameter.", diff --git a/subworkflows/local/clonal_analysis.nf b/subworkflows/local/clonal_analysis.nf index ff4afacf..2907fa2a 100644 --- a/subworkflows/local/clonal_analysis.nf +++ b/subworkflows/local/clonal_analysis.nf @@ -51,13 +51,14 @@ workflow CLONAL_ANALYSIS { .dump(tag: 'ch_find_threshold_samplesheet') .collectFile(name: 'find_threshold_samplesheet.txt', newLine: true) - REPORT_THRESHOLD ( - ch_find_threshold, - ch_logo, - ch_find_threshold_samplesheet - ) - ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions) - + if !(params.skip_report_threshold){ + REPORT_THRESHOLD ( + ch_find_threshold, + ch_logo, + ch_find_threshold_samplesheet + ) + ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions) + } } // prepare ch for define clones