Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix(TYPO): index_alignement should be index_alignment #1506

Merged
merged 4 commits into from
May 7, 2024
Merged

fix(TYPO): index_alignement should be index_alignment #1506

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
4bbc7c2
fix(TYPO): index_alignement should be index_alignment
nh13 May 7, 2024
6eb8943
Update CHANGELOG.md
maxulysse May 7, 2024
551cf08
Merge branch 'dev' into nh13-index-alignment-typo
maxulysse May 7, 2024
21e216e
Merge branch 'dev' into nh13-index-alignment-typo
maxulysse May 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions workflows/sarek/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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, [] ] }
Expand Down Expand Up @@ -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
Expand Down
Loading