align-DNA v8.1.0
Changed
- Fix
sort_order
definition - Remove
run_index_SAMtools
, output index duringrun_merge_SAMtools
instead - Update
README.md
: fix links, format code, grammar - Remove sample name from
output_dir
intemplate.config
- Update PR template to follow here
- Remove
bam_output_dir
frommain.nf
since it is not used, undefined and causes warning - Change "shell" to "script" in processes
- Move
F16.config
to config folder - Rename process
Generate_Sha512sum
togenerate_sha512sum
- Rename process
run_validate
torun_validate_PipeVal
- Restructure repo to follow template
- Rename
align-DNA.nf
tomain.nf
- Change output directory of MarkDuplicatesSpark metrics file to '/QC'.
- Use SAMtools
sort
instead of PicardSortSam
Added
- Add
retry
method torun_sort_SAMtools
andrun_MarkDuplicatesSpark_GATK
(if run out of RAM then retry with more memory) - Add process
run_merge_SAMtools
: use whenparams.mark_duplicates=false
to ensure multiple BAM outputs are merged .github/CODEOWNERS
- Add config file for F16 node
- Use SAMtools index in the case MarkDuplicates (set by mark_duplicates parameter) is false
- Add parameter to toggle Spark metric generation. Default is off.
Full Changelog: v8.0.0...v8.1.0