Merge remote-tracking branch 'upstream/dev' into dev-checkm2

nf-core · Oct 31, 2024 · 0ebab07 · 0ebab07
2 parents 76dac5c + cd5ebae
commit 0ebab07
Show file tree

Hide file tree

Showing 5 changed files with 37 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,11 +8,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#707](https://github.com/nf-core/mag/pull/707) - Added CheckM2 as an alternative bin completeness and QC tool (added by @dialvarezs)
+- [#708](https://github.com/nf-core/mag/pull/708) - Added `--exclude_unbins_from_postbinning` parameter to exclude unbinned contigs from post-binning processes, speeding up Prokka in some cases (added by @dialvarezs)
 
 ### `Changed`
 
 ### `Fixed`
 
+- [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs)
+
+### `Dependencies`
+
+### `Deprecated`
+
+## 3.2.1 [2024-10-30]
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+- [#707](https://github.com/nf-core/mag/pull/674) - Fix missing space resulting in malformed args for MEGAHIT (reported by @d4straub, fix by @jfy133)
+
 ### `Dependencies`
 
 | Tool    | Previous version | New version |

diff --git a/conf/modules.config b/conf/modules.config
@@ -257,7 +257,7 @@ process {
     }
 
     withName: MEGAHIT {
-        ext.args   = { params.megahit_options ? params.megahit_options + "-m ${task.memory.toBytes()}" : "-m ${task.memory.toBytes()}" }
+        ext.args   = { params.megahit_options ? params.megahit_options + " -m ${task.memory.toBytes()}" : "-m ${task.memory.toBytes()}" }
         ext.prefix = { "MEGAHIT-${meta.id}" }
         publishDir = [path: { "${params.outdir}/Assembly/MEGAHIT" }, mode: params.publish_dir_mode, pattern: "*.{fa.gz,log}"]
     }

diff --git a/nextflow.config b/nextflow.config
@@ -121,6 +121,7 @@ params {
     refine_bins_dastool             = false
     refine_bins_dastool_threshold   = 0.5
     postbinning_input               = 'raw_bins_only'
+    exclude_unbins_from_postbinning   = false
 
     // Bin QC
     skip_binqc                           = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -704,6 +704,12 @@
                     "type": "integer",
                     "default": 3000,
                     "description": "Minimum contig length for Tiara to use for domain classification. For accurate classification, should be longer than 3000 bp."
+                },
+                "exclude_unbins_from_postbinning": {
+                    "type": "boolean",
+                    "description": "Exclude unbinned contigs in the post-binning steps (bin QC, taxonomic classification, and annotation steps).",
+                    "help": "If you're not interested in assemby results that are not considered 'genome level', excluding unbinned contigs can greatly speed up downstream steps such as Prokka, that can be quite slow and spin up many tasks.",
+                    "default": false
                 }
             }
         },

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -782,15 +782,19 @@ workflow MAG {
             ch_input_for_postbinning_bins_unbins = ch_binning_results_bins.mix(ch_binning_results_unbins)
         }
 
-        DEPTHS(ch_input_for_postbinning_bins_unbins, BINNING.out.metabat2depths, ch_short_reads)
+        ch_input_for_postbinning = params.exclude_unbins_from_postbinning
+            ? ch_input_for_postbinning_bins
+            : ch_input_for_postbinning_bins_unbins
+
+        DEPTHS(ch_input_for_postbinning, BINNING.out.metabat2depths, ch_short_reads)
         ch_input_for_binsummary = DEPTHS.out.depths_summary
         ch_versions = ch_versions.mix(DEPTHS.out.versions)
 
         /*
         * Bin QC subworkflows: for checking bin completeness with either BUSCO, CHECKM, CHECKM2, and/or GUNC
         */
 
-        ch_input_bins_for_qc = ch_input_for_postbinning_bins_unbins.transpose()
+        ch_input_bins_for_qc = ch_input_for_postbinning.transpose()
 
         BIN_QC(
             ch_input_bins_for_qc,
@@ -802,7 +806,7 @@ workflow MAG {
         ch_versions = ch_versions.mix(BIN_QC.out.versions)
 
         if (params.run_gunc) {
-            ch_input_bins_for_gunc = ch_input_for_postbinning_bins_unbins.filter { meta, bins ->
+            ch_input_bins_for_gunc = ch_input_for_postbinning.filter { meta, bins ->
                 meta.domain != "eukarya"
             }
 
@@ -817,7 +821,7 @@ workflow MAG {
 
         ch_quast_bins_summary = Channel.empty()
         if (!params.skip_quast) {
-            ch_input_for_quast_bins = ch_input_for_postbinning_bins_unbins
+            ch_input_for_quast_bins = ch_input_for_postbinning
                 .groupTuple()
                 .map { meta, bins ->
                     def new_bins = bins.flatten()
@@ -846,7 +850,7 @@ workflow MAG {
             ch_cat_db = CAT_DB_GENERATE.out.db
         }
         CAT(
-            ch_input_for_postbinning_bins_unbins,
+            ch_input_for_postbinning,
             ch_cat_db
         )
         // Group all classification results for each sample in a single file
@@ -877,7 +881,7 @@ workflow MAG {
             ch_gtdbtk_summary = Channel.empty()
             if (gtdb) {
 
-                ch_gtdb_bins = ch_input_for_postbinning_bins_unbins.filter { meta, bins ->
+                ch_gtdb_bins = ch_input_for_postbinning.filter { meta, bins ->
                     meta.domain != "eukarya"
                 }
 
@@ -911,7 +915,7 @@ workflow MAG {
          */
 
         if (!params.skip_prokka) {
-            ch_bins_for_prokka = ch_input_for_postbinning_bins_unbins
+            ch_bins_for_prokka = ch_input_for_postbinning
                 .transpose()
                 .map { meta, bin ->
                     def meta_new = meta + [id: bin.getBaseName()]
@@ -930,7 +934,7 @@ workflow MAG {
         }
 
         if (!params.skip_metaeuk && (params.metaeuk_db || params.metaeuk_mmseqs_db)) {
-            ch_bins_for_metaeuk = ch_input_for_postbinning_bins_unbins
+            ch_bins_for_metaeuk = ch_input_for_postbinning
                 .transpose()
                 .filter { meta, bin ->
                     meta.domain in ["eukarya", "unclassified"]