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

Patch release: Fix #449 (wrong contigs from aDNA workflow going to binning) #458

Merged
merged 7 commits into from
Jun 19, 2023
Merged

Patch release: Fix #449 (wrong contigs from aDNA workflow going to binning) #458

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
ef5d433
fix Genome binning is performed on uncorrected contigs when selecting…
maxibor Jun 14, 2023
b744d27
Apply suggestions from code review
jfy133 Jun 15, 2023
9b619ad
Update workflows/mag.nf
jfy133 Jun 15, 2023
2af6cff
bump version and update changelog
maxibor Jun 19, 2023
fd826ba
Apply suggestions from code review
jfy133 Jun 19, 2023
35d9489
integrated changes of #449 into this PR
maxibor Jun 19, 2023
9f86e7d
451 not 449
maxibor Jun 19, 2023
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
10 changes: 1 addition & 9 deletions subworkflows/local/binning_refinement.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,22 +22,14 @@ def getColNo(filename) {

workflow BINNING_REFINEMENT {
take:
contigs
ch_contigs_for_dastool // channel: [ val(meta), path(contigs) ]
bins // channel: [ val(meta), path(bins) ]
depths
reads

main:
ch_versions = Channel.empty()

// Drop unnecessary files
ch_contigs_for_dastool = contigs
.map {
meta, assembly, bams, bais ->
def meta_new = meta.clone()
[ meta_new, assembly ]
}

ch_bins_for_fastatocontig2bin = RENAME_PREDASTOOL(bins).renamed_bins
.branch {
metabat2: it[0]['binner'] == 'MetaBAT2'
Expand Down
9 changes: 8 additions & 1 deletion workflows/mag.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -581,7 +581,14 @@ workflow MAG {
// If any two of the binners are both skipped at once, do not run because DAS_Tool needs at least one
if ( params.refine_bins_dastool ) {

BINNING_REFINEMENT ( BINNING_PREPARATION.out.grouped_mappings, BINNING.out.bins, BINNING.out.metabat2depths, ch_short_reads )
if (params.ancient_dna) {
contigs_ch = ANCIENT_DNA_ASSEMLY_VALIDATION.out.contigs_recalled
jfy133 marked this conversation as resolved.
Show resolved Hide resolved
} else {
contigs_ch = BINNING_PREPARATION.out.grouped_mappings
.map{ meta, contigs, bam, bai -> [ meta, contigs ] }
}

BINNING_REFINEMENT ( contigs_ch, BINNING.out.bins, BINNING.out.metabat2depths, ch_short_reads )
ch_versions = ch_versions.mix(BINNING_REFINEMENT.out.versions)

if ( params.postbinning_input == 'raw_bins_only' ) {
Expand Down