Closed JoseEspinosa closed 2 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit e53da35
+| ✅ 220 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 5 tests had warnings |!
Maybe we could also implement --skip_merged_replicate_bigwig
parameter? So that the subworkflow MERGED_REPLICATE_BAM_TO_BIGWIG
can be skipped?
Maybe we could also implement
--skip_merged_replicate_bigwig
parameter? So that the subworkflowMERGED_REPLICATE_BAM_TO_BIGWIG
can be skipped?
that sounds like a good idea too.
As reported in #344, the
bedtools sort
command in theBEDTOOL_GENOMECOV
process is memory-greedy when dealing with merged replicates. Here, the default memory is increased and sorting is performed using the bashsort
command which should alleviate also the problem as it takes into account the memory available and uses temporary files, if needed.PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).CHANGELOG.md
is updated.