Add binner COMEBin

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#873](https://github.com/nf-core/mag/pull/873) - Document usage of `longread_percentidentity` and `shortread_percentidentity` and set the value of `longread_percentidentity` in the `test_full` profile to 85 (by @prototaxites)
+- [#875](https://github.com/nf-core/mag/pull/875) - Add binner COMEBin (by @d4straub)
 
 ### `Changed`
 

conf/modules.config

@@ -806,6 +806,23 @@ process {
         ext.prefix = { "${meta.assembler}-CONCOCT-${meta.id}" }
     }
 
+    withName: COMEBIN_RUNCOMEBIN {
+        publishDir = [
+            [
+                path: { "${params.outdir}/GenomeBinning/COMEBin/stats/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{log,tsv}',
+            ],
+            [
+                path: { "${params.outdir}/GenomeBinning/COMEBin/bins/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fa.gz',
+            ],
+        ]
+        ext.prefix = { "${meta.assembler}-COMEBin-${meta.id}" }
+        // ext.args = "-b 20" // default value fails with "-profile test" (100 passes that step) as in https://github.com/ziyewang/COMEBin/issues/4 but the binner fails later after: "[CheckM - analyze] Identifying marker genes in bins."
+    }
+
     withName: SEQKIT_STATS {
         ext.args   = ""
         publishDir = [enabled: false]
@@ -827,6 +844,10 @@ process {
         ext.prefix = { "${meta.assembler}-CONCOCT-${meta.id}" }
     }
 
+    withName: DASTOOL_FASTATOCONTIG2BIN_COMEBIN {
+        ext.prefix = { "${meta.assembler}-COMEBin-${meta.id}" }
+    }
+
     withName: DASTOOL_FASTATOCONTIG2BIN_TIARA {
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.id}" }
     }

conf/test.config

@@ -28,6 +28,7 @@ params {
     max_unbinned_contigs        = 2
     // Including (even length filtered) CONOCT bins adds another 5 minutes, so we skip it in the default test (testing in assemblyinput)
     skip_concoct                = true
+    skip_comebin                = true
     busco_db                    = params.pipelines_testdata_base_path + 'mag/databases/busco/bacteria_odb10.2024-01-08.tar.gz'
     busco_db_lineage            = 'bacteria_odb10'
     busco_clean                 = true

conf/test_alternatives.config

@@ -36,6 +36,7 @@ params {
     skip_gtdbtk                = true
     skip_maxbin2               = true
     skip_concoct               = true
+    skip_comebin               = true
     skip_metaeuk               = true
     megahit_fix_cpu_1          = true
 }

conf/test_assembly_input.config

@@ -42,6 +42,7 @@ params {
     skip_prokka                     = true
     skip_gtdbtk                     = true
     skip_concoct                    = false
+    skip_comebin                    = true
 
     refine_bins_dastool             = true
     refine_bins_dastool_threshold   = 0.0

conf/test_hybrid.config

@@ -38,6 +38,7 @@ params {
     skip_metamdbg                 = true
     skip_gtdbtk                   = true
     skip_concoct                  = true
+    skip_comebin                  = true
 
     spadeshybrid_fix_cpus         = 2
 }

conf/test_longreadonly.config

@@ -37,4 +37,5 @@ params {
 
     skip_gtdbtk                = true
     skip_concoct               = true
+    skip_comebin               = true
 }

conf/test_longreadonly_alternatives.config

@@ -37,5 +37,6 @@ params {
     skip_prokka                   = true
     skip_gtdbtk                   = true
     skip_concoct                  = true
+    skip_comebin                  = true
     skip_metaeuk                  = true
 }

conf/test_minimal.config

@@ -40,6 +40,7 @@ params {
     skip_metabat2                 = true
     skip_maxbin2                  = true
     skip_concoct                  = true
+    skip_comebin                  = true
     skip_prokka                   = true
     skip_binqc                    = true
     skip_gtdbtk                   = true

conf/test_single_end.config

@@ -39,6 +39,7 @@ params {
     bcftools_view_high_variant_quality   = 0
     bcftools_view_medium_variant_quality = 0
     bcftools_view_minimal_allelesupport  = 3
+    skip_comebin                         = true
     min_length_unbinned_contigs          = 1000000
     max_unbinned_contigs                 = 2
     binqc_tool                           = 'checkm'

modules.json

@@ -96,6 +96,11 @@
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
+                    "comebin/runcomebin": {
+                        "branch": "master",
+                        "git_sha": "b153ee540a64472fef22a0699040238dcd422bfc",
+                        "installed_by": ["modules"]
+                    },
                     "concoct/concoct": {
                         "branch": "master",
                         "git_sha": "ff39793aeff17b7ccb107424215898710b4aa424",