Merge pull request #463 from nf-core/master-to-dev

Pull in recent patch release changes from master into dev
nf-core · Jul 4, 2023 · 0906f13 · 0906f13
2 parents 36aa11b + 6da700a
commit 0906f13
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.3.1dev - [date]
+## 2.4.0dev - [date]
 
 ### `Added`
 
@@ -39,6 +39,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | BCFtools | 1.16             | 1.17        |
 | SAMtools | 1.16.1           | 1.17        |
 
+## v2.3.2 - [2023-06-23]
+
+### `Fixed`
+
+- [#461](https://github.com/nf-core/mag/pull/461) - Fix full-size AWS test profile paths (by @jfy133)
+- [#461](https://github.com/nf-core/mag/pull/461) - Fix pyDamage results being overwritten (reported by @alexhbnr, fix by @jfy133)
+
+## v2.3.1 - [2023-06-19]
+
+### `Fixed`
+
+- [#458](https://github.com/nf-core/mag/pull/458) - Correct the major issue in ancient DNA workflow of binning refinement being performed on uncorrected contigs instead of aDNA consensus recalled contigs (issue [#449](https://github.com/nf-core/mag/issues/449))
+- [#451](https://github.com/nf-core/mag/pull/451) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in [#458](https://github.com/nf-core/mag/pull/458) )
+
 ## v2.3.0 - [2023/03/02]
 
 ### `Added`

diff --git a/conf/modules.config b/conf/modules.config
@@ -493,8 +493,8 @@ process {
     }
 
     withName: BCFTOOLS_VIEW {
-        ext.args   = "-v snps,mnps -i 'QUAL>=${params.bcftools_view_high_variant_quality} || (QUAL>=${params.bcftools_view_medium_variant_quality} && FORMAT/AO>=${params.bcftools_view_minimal_allelesupport})'"
         ext.prefix = { "${meta.assembler}-${meta.id}.filtered" }
+        ext.args   = "-v snps,mnps -i 'QUAL>=${params.bcftools_view_high_variant_quality} || (QUAL>=${params.bcftools_view_medium_variant_quality} && FORMAT/AO>=${params.bcftools_view_minimal_allelesupport})'"
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/variant_calling/filtered" },
             mode: params.publish_dir_mode,
@@ -524,7 +524,7 @@ process {
     withName: PYDAMAGE_ANALYZE {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }
@@ -533,7 +533,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }

diff --git a/lib/WorkflowMag.groovy b/lib/WorkflowMag.groovy
@@ -18,6 +18,9 @@ class WorkflowMag {
         if (params.coassemble_group && params.binning_map_mode == 'own') {
             Nextflow.error("Invalid combination of parameter '--binning_map_mode own' and parameter '--coassemble_group'. Select either 'all' or 'group' mapping mode when performing group-wise co-assembly.")
         }
+        if (params.ancient_dna && params.binning_map_mode != 'own') {
+            Nextflow.error("Invalid combination of parameter '--binning_map_mode' and parameter '--ancient_dna'. Ancient DNA mode can only be executed with --binning_map_mode own. You supplied: --binning_map_mode ${params.binning_map_mode}")
+        }
 
         // Check if specified cpus for SPAdes are available
         if ( params.spades_fix_cpus > params.max_cpus ) {

diff --git a/nextflow.config b/nextflow.config
@@ -62,7 +62,7 @@ params {
     // ancient DNA assembly validation options
     ancient_dna                          = false
     pydamage_accuracy                    = 0.5
-    skip_ancient_damagecorrection         = false
+    skip_ancient_damagecorrection        = false
     freebayes_ploidy                     = 1
     freebayes_min_basequality            = 20
     freebayes_minallelefreq              = 0.33
@@ -348,7 +348,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.3.1dev'
+    version         = '2.4.0dev'
     doi             = '10.1093/nargab/lqac007'
 }
 

diff --git a/subworkflows/local/binning_preparation.nf b/subworkflows/local/binning_preparation.nf
@@ -28,6 +28,7 @@ workflow BINNING_PREPARATION {
             .map { group, assembly_meta, assembly, index, reads_meta, reads -> [ assembly_meta, assembly, index, reads_meta, reads ] }
 
     } else {
+        // i.e. --binning_map_mode 'own'
         // combine assemblies (not co-assembled) with reads from own sample
         ch_reads_bowtie2 = reads.map{ meta, reads -> [ meta.id, meta, reads ] }
         ch_bowtie2_input = BOWTIE2_ASSEMBLY_BUILD.out.assembly_index

diff --git a/subworkflows/local/binning_refinement.nf b/subworkflows/local/binning_refinement.nf
@@ -15,7 +15,7 @@ include { RENAME_POSTDASTOOL                                              } from
 
 workflow BINNING_REFINEMENT {
     take:
-    contigs
+    ch_contigs_for_dastool // channel: [ val(meta), path(contigs) ]
     bins           // channel: [ val(meta), path(bins) ]
 
     main:
@@ -25,19 +25,15 @@ workflow BINNING_REFINEMENT {
     // everything here is either unclassified or a prokaryote
     ch_bins = bins
         .map { meta, bins ->
-            meta_new = meta.clone()
-            meta_new.remove('domain')
+            def meta_new = meta - meta.subMap('domain')
             [meta_new, bins]
         }
+        .groupTuple()
+        .map {
+            meta, bins -> [meta, bins.flatten()]
+        }
 
-    // Drop unnecessary files
-    ch_contigs_for_dastool = contigs
-                                .map {
-                                    meta, assembly, bams, bais ->
-                                        def meta_new = meta.clone()
-                                        [ meta_new, assembly ]
-                                }
-
+    // prepare bins
     ch_bins_for_fastatocontig2bin = RENAME_PREDASTOOL(ch_bins).renamed_bins
                                         .branch {
                                             metabat2: it[0]['binner'] == 'MetaBAT2'

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -641,7 +641,8 @@ workflow MAG {
 
     if (!params.skip_binning){
 
-        if (params.ancient_dna && params.run_ancient_damagecorrection) {
+        // Make sure if running aDNA subworkflow to use the damage-corrected contigs for higher accuracy
+        if (params.ancient_dna && !params.skip_ancient_damagecorrection) {
             BINNING (
                 BINNING_PREPARATION.out.grouped_mappings
                     .join(ANCIENT_DNA_ASSEMBLY_VALIDATION.out.contigs_recalled)
@@ -656,10 +657,20 @@ workflow MAG {
         }
 
         if ( params.bin_domain_classification ) {
-            DOMAIN_CLASSIFICATION ( ch_assemblies, BINNING.out.bins, BINNING.out.unbinned )
+
+            // Make sure if running aDNA subworkflow to use the damage-corrected contigs for higher accuracy
+            if (params.ancient_dna && !params.skip_ancient_damagecorrection) {
+                ch_assemblies_for_domainclassification = ANCIENT_DNA_ASSEMBLY_VALIDATION.out.contigs_recalled
+            } else {
+                ch_assemblies_for_domainclassification = ch_assemblies
+            }
+
+            DOMAIN_CLASSIFICATION ( ch_assemblies_for_domainclassification, BINNING.out.bins, BINNING.out.unbinned )
             ch_binning_results_bins   = DOMAIN_CLASSIFICATION.out.classified_bins
             ch_binning_results_unbins = DOMAIN_CLASSIFICATION.out.classified_unbins
             ch_versions               = ch_versions.mix(DOMAIN_CLASSIFICATION.out.versions)
+
+
         } else {
             ch_binning_results_bins = BINNING.out.bins
                 .map { meta, bins ->
@@ -694,7 +705,14 @@ workflow MAG {
                     meta.domain == "eukarya"
                 }
 
-            BINNING_REFINEMENT ( BINNING_PREPARATION.out.grouped_mappings, ch_prokarya_bins_dastool )
+            if (params.ancient_dna) {
+                ch_contigs_for_binrefinement = ANCIENT_DNA_ASSEMBLY_VALIDATION.out.contigs_recalled
+            } else {
+                ch_contigs_for_binrefinement = BINNING_PREPARATION.out.grouped_mappings
+                    .map{ meta, contigs, bam, bai -> [ meta, contigs ] }
+            }
+
+            BINNING_REFINEMENT ( ch_contigs_for_binrefinement, ch_prokarya_bins_dastool )
 
             ch_refined_bins = ch_eukarya_bins_dastool.mix(BINNING_REFINEMENT.out.refined_bins)
             ch_refined_unbins = BINNING_REFINEMENT.out.refined_unbins