From b0fb148b4a8b78ab218c7867d29807f3f9243bcb Mon Sep 17 00:00:00 2001 From: Benjamin Wingfield Date: Mon, 1 Jul 2024 16:13:15 +0100 Subject: [PATCH 1/2] write only mandatory pvar columns --- modules/local/plink2_relabelpvar.nf | 2 +- modules/local/plink2_vcf.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/plink2_relabelpvar.nf b/modules/local/plink2_relabelpvar.nf index 6e5cb2ce..5298d5d2 100644 --- a/modules/local/plink2_relabelpvar.nf +++ b/modules/local/plink2_relabelpvar.nf @@ -51,7 +51,7 @@ process PLINK2_RELABELPVAR { --set-all-var-ids '@:#:\$r:\$a' \\ $set_ma_missing \\ --pfile ${geno.baseName} $compressed \\ - --make-just-pvar zs \\ + --make-just-pvar zs cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \\ --out $output # -a: cross platform (mac, linux) method of preserving symlinks diff --git a/modules/local/plink2_vcf.nf b/modules/local/plink2_vcf.nf index 428d5cde..297a5dea 100644 --- a/modules/local/plink2_vcf.nf +++ b/modules/local/plink2_vcf.nf @@ -50,7 +50,7 @@ process PLINK2_VCF { $args \\ --vcf $vcf $dosage_options \\ --allow-extra-chr $chrom_filter \\ - --make-pgen vzs \\ + --make-pgen vzs pvar-cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \\ --out ${output} gzip ${output}.vmiss From c13f7220147ffc887eddaee1ad2ced7652491f86 Mon Sep 17 00:00:00 2001 From: Sam Lambert Date: Thu, 20 Jun 2024 10:13:06 +0100 Subject: [PATCH 2/2] Fix samplesheet parsing error warnings (#322) * Update SamplesheetParser.groovy * fix multiple samplesheet error message --------- Co-authored-by: Benjamin Wingfield --- lib/SamplesheetParser.groovy | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/SamplesheetParser.groovy b/lib/SamplesheetParser.groovy index 828170a7..e3e41299 100644 --- a/lib/SamplesheetParser.groovy +++ b/lib/SamplesheetParser.groovy @@ -168,7 +168,7 @@ class SamplesheetParser { def samplesets = rows.collect { row -> row.sampleset } def n_samplesets = samplesets.toSet().size() if (n_samplesets > 1) { - Nextflow.error("${n_samplesets} missing chromosomes detected! Maximum is 1. Check your samplesheet.") + Nextflow.error("${n_samplesets} samplesets detected! Maximum is 1. Check your samplesheet.") } } @@ -177,7 +177,7 @@ class SamplesheetParser { def n_bad_name = samplesets.count { it == "reference" | it.contains("_") } if (n_bad_name != 0) { - Nextflow.error("Reserved sampleset name detected. Please don't call your sampleset 'reference'") + Nextflow.error("Reserved sampleset name/character detected. DO NOT call your sampleset 'reference' or use underscores ('_') in the name.") } }