From 4bbc7c29469005d268ce6411b35d63fcc3f54385 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 6 May 2024 22:57:41 -0700 Subject: [PATCH 1/2] fix(TYPO): index_alignement should be index_alignment --- main.nf | 4 ++-- workflows/sarek/main.nf | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index 93f896d6b9..9c272624fb 100755 --- a/main.nf +++ b/main.nf @@ -162,7 +162,7 @@ workflow NFCORE_SAREK { : PREPARE_GENOME.out.hashtable // Gather index for mapping given the chosen aligner - index_alignement = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa : + index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa : aligner == "bwa-mem2" ? bwamem2 : dragmap @@ -279,7 +279,7 @@ workflow NFCORE_SAREK { gc_file, germline_resource, germline_resource_tbi, - index_alignement, + index_alignment, intervals_and_num_intervals, intervals_bed_combined, intervals_bed_combined_for_variant_calling, diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index d28aabff4c..164a44f45e 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -106,7 +106,7 @@ workflow SAREK { gc_file germline_resource germline_resource_tbi - index_alignement + index_alignment intervals_and_num_intervals intervals_bed_combined intervals_bed_combined_for_variant_calling @@ -188,7 +188,7 @@ workflow SAREK { input_fastq, fasta, fasta_fai, - index_alignement, + index_alignment, params.group_by_umi_strategy) bam_converted_from_fastq = FASTQ_CREATE_UMI_CONSENSUS_FGBIO.out.consensusbam.map{ meta, bam -> [ meta, bam, [] ] } @@ -255,7 +255,7 @@ workflow SAREK { // reads will be sorted sort_bam = true - FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignement, sort_bam, fasta, fasta_fai) + FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai) // Grouping the bams from the same samples not to stall the workflow // Use groupKey to make sure that the correct group can advance as soon as it is complete From 6eb89435e8639a188ebe8b124715a5766962a0ad Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 11:00:09 +0200 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63944eaf64..b96762f898 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` - [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` +- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`) ### Fixed