Merge pull request #1506 from nf-core/nh13-index-alignment-typo

fix(TYPO): index_alignement should be index_alignment
nf-core · May 7, 2024 · 448a4d9 · 448a4d9
2 parents 9ec46ca + 21e216e
commit 448a4d9
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is
 - [#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`
 - [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md
+- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`)
 - [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors
 
 ### Fixed

diff --git 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
@@ -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