From 7f2e86bdd874041163159635b7fc89a198e198c4 Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Tue, 14 Jun 2022 12:27:09 +0200 Subject: [PATCH 1/3] added skip-scorpio parma fixes #234 --- nextflow.config | 1 + poreCov.nf | 4 +++- workflows/process/pangolin.nf | 3 ++- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index af0d611..bd81272 100644 --- a/nextflow.config +++ b/nextflow.config @@ -48,6 +48,7 @@ params { lcs_cutoff = 0.03 defaultpangolin = 'nanozoo/pangolin-v4:4.0.4--1.2.133' defaultnextclade = 'nanozoo/nextclade:1.11.0--2022-03-31' + pangolin_skip_scorpio = false // parameters primerV = 'V3' diff --git a/poreCov.nf b/poreCov.nf index e73a72a..8faa0e7 100755 --- a/poreCov.nf +++ b/poreCov.nf @@ -476,7 +476,9 @@ ${c_yellow}Workflow control (optional)${c_reset} --nanopolish use nanopolish instead of medaka for ARTIC (needs --fast5) to skip basecalling use --fastq or --fastq_pass and provide a sequencing_summary.txt in addition to --fast5 e.g --nanopolish sequencing_summary.txt - --screen_reads Determines the Pangolineage of each individual read (takes time) + --screen_reads Determines the Pangolineage of each individual read (takes time) + --pangolin_skip_scorpio Skip Scorpio in pangolin run [default: $params.pangolin_skip_scorpio] + ${c_dim}From pangolin version 4, Scorpio overwrites Usher results which leads to many unassigned samples${c_reset} ${c_yellow}Parameters - Lineage detection on reads (see screen_reads, optional)${c_reset} --lcs_ucsc_version Create marker table based on a specific UCSC SARS-CoV-2 tree (e.g. '2022-05-01'). Use 'predefined' diff --git a/workflows/process/pangolin.nf b/workflows/process/pangolin.nf index 089895a..8102487 100644 --- a/workflows/process/pangolin.nf +++ b/workflows/process/pangolin.nf @@ -7,8 +7,9 @@ process pangolin { output: tuple val(name), path("lineage_report_${name}.csv") optional true script: + def args = params.pangolin_skip_scorpio ? '--skip-scorpio' : '' """ - pangolin -t ${task.cpus} ${fasta} + pangolin ${args} -t ${task.cpus} ${fasta} mv lineage_report.csv lineage_report_${name}.csv From 589147d189e66feb27d3755460576cf154780a68 Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Wed, 15 Jun 2022 13:11:41 +0200 Subject: [PATCH 2/3] changed default to true --- nextflow.config | 2 +- poreCov.nf | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index bd81272..39d08ff 100644 --- a/nextflow.config +++ b/nextflow.config @@ -48,7 +48,7 @@ params { lcs_cutoff = 0.03 defaultpangolin = 'nanozoo/pangolin-v4:4.0.4--1.2.133' defaultnextclade = 'nanozoo/nextclade:1.11.0--2022-03-31' - pangolin_skip_scorpio = false + pangolin_skip_scorpio = true // parameters primerV = 'V3' diff --git a/poreCov.nf b/poreCov.nf index 8faa0e7..081c52d 100755 --- a/poreCov.nf +++ b/poreCov.nf @@ -478,7 +478,8 @@ ${c_yellow}Workflow control (optional)${c_reset} e.g --nanopolish sequencing_summary.txt --screen_reads Determines the Pangolineage of each individual read (takes time) --pangolin_skip_scorpio Skip Scorpio in pangolin run [default: $params.pangolin_skip_scorpio] - ${c_dim}From pangolin version 4, Scorpio overwrites Usher results which leads to many unassigned samples${c_reset} + ${c_dim}From pangolin version 4, Scorpio overwrites Usher results which leads to many unassigned samples + Can be turned of with --pangolin_skip_scorpio false${c_reset} ${c_yellow}Parameters - Lineage detection on reads (see screen_reads, optional)${c_reset} --lcs_ucsc_version Create marker table based on a specific UCSC SARS-CoV-2 tree (e.g. '2022-05-01'). Use 'predefined' From 6f0dc2d857a2034323f2157e0a7ae35b2da3737e Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Fri, 17 Jun 2022 15:09:39 +0200 Subject: [PATCH 3/3] renamed param --- nextflow.config | 2 +- poreCov.nf | 4 ++-- workflows/process/pangolin.nf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 39d08ff..2cae9bd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -48,7 +48,7 @@ params { lcs_cutoff = 0.03 defaultpangolin = 'nanozoo/pangolin-v4:4.0.4--1.2.133' defaultnextclade = 'nanozoo/nextclade:1.11.0--2022-03-31' - pangolin_skip_scorpio = true + scorpio = false // parameters primerV = 'V3' diff --git a/poreCov.nf b/poreCov.nf index 081c52d..7bb9b60 100755 --- a/poreCov.nf +++ b/poreCov.nf @@ -477,9 +477,9 @@ ${c_yellow}Workflow control (optional)${c_reset} to skip basecalling use --fastq or --fastq_pass and provide a sequencing_summary.txt in addition to --fast5 e.g --nanopolish sequencing_summary.txt --screen_reads Determines the Pangolineage of each individual read (takes time) - --pangolin_skip_scorpio Skip Scorpio in pangolin run [default: $params.pangolin_skip_scorpio] + --scorpio Skip Scorpio in pangolin run [default: $params.scorpio] ${c_dim}From pangolin version 4, Scorpio overwrites Usher results which leads to many unassigned samples - Can be turned of with --pangolin_skip_scorpio false${c_reset} + Can be turned on with --scorpio${c_reset} ${c_yellow}Parameters - Lineage detection on reads (see screen_reads, optional)${c_reset} --lcs_ucsc_version Create marker table based on a specific UCSC SARS-CoV-2 tree (e.g. '2022-05-01'). Use 'predefined' diff --git a/workflows/process/pangolin.nf b/workflows/process/pangolin.nf index 8102487..dd59d78 100644 --- a/workflows/process/pangolin.nf +++ b/workflows/process/pangolin.nf @@ -7,7 +7,7 @@ process pangolin { output: tuple val(name), path("lineage_report_${name}.csv") optional true script: - def args = params.pangolin_skip_scorpio ? '--skip-scorpio' : '' + def args = params.scorpio ? '' : '--skip-scorpio' """ pangolin ${args} -t ${task.cpus} ${fasta}