From 2b034da9d26d333df9bda559c79f82f775fa891f Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 18 Jul 2022 16:40:22 +0200 Subject: [PATCH 1/3] Allow any step but annotation to start from bam-files --- workflows/sarek.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index bfc40004d0..21e7a11e1e 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -1150,9 +1150,9 @@ def extract_csv(csv_file) { meta.size = 1 // default number of splitted fastq - if (params.step == 'mapping') return [meta, bam, bai] + if (params.step != 'annotate') return [meta, bam, bai] else { - log.error "Samplesheet contains ubam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations" + log.error "Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations" System.exit(1) } From 783b4d2d3eeece1a9ae5d603b07fb465754ae8a3 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 18 Jul 2022 20:48:20 +0200 Subject: [PATCH 2/3] Updating changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49943ad938..74ba835a62 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -142,6 +142,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools - [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic - [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks +- [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files + ### Deprecated From 9be3c5c011ab7b7b4f3aba1c53358b34558acc53 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 18 Jul 2022 21:18:38 +0200 Subject: [PATCH 3/3] Removing redundant blank line --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74ba835a62..106c24c75d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -144,7 +144,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks - [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files - ### Deprecated ### Removed