Merge pull request #602 from maxibor/adna_binning_group

feat: allow adna co-binning

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#581](https://github.com/nf-core/mag/pull/581) - Added explicit licence text to headers of all custom scripts (reported by @FriederikeHanssen and @maxibor, fix by @jfy133)
+- [#602](https://github.com/nf-core/mag/pull/602) - Co-binning when using aDNA mode now enabled (added by @maxibor)
 
 ### `Fixed`
 

lib/WorkflowMag.groovy

@@ -19,9 +19,6 @@ 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 ) {

subworkflows/local/ancient_dna.nf

@@ -12,7 +12,14 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
     main:
         ch_versions = Channel.empty()
 
-        PYDAMAGE_ANALYZE(input.map {item -> [item[0], item[2], item[3]]})
+        PYDAMAGE_ANALYZE(
+            input.map {
+                meta, contigs, bam, bai -> [
+                    meta, bam[0], bai[0]
+                ]
+            }
+        )
+
         PYDAMAGE_FILTER(PYDAMAGE_ANALYZE.out.csv)
         ch_versions = ch_versions.mix(PYDAMAGE_ANALYZE.out.versions.first())