Bbnorm minid

CHANGELOG.md

@@ -3,10 +3,11 @@
 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).
 
-## v1.1.0 - [date]
+## v1.1.0dev - [date]
 
 ### `Added`
 
+- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module. Now the threshold for mapping a read to a contig is an identity of 0.9. The previous version of nf-core/metatdenovo used the default for BBMap, 0.76. This version might hence give slightly different results than the previous.
 - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules
 
 ### `Changed`

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/releases/tag/1.0.1" target="_blank">nf-core/metatdenovo</a>
+  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/tree/dev" target="_blank">nf-core/metatdenovo</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/metatdenovo/1.0.1/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/metatdenovo/dev/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-metatdenovo-methods-description":

conf/modules.config

@@ -102,7 +102,7 @@ process {
     }
 
     withName: BBMAP_ALIGN {
-        ext.args = "trimreaddescriptions=t pigz=t"
+        ext.args = { "trimreaddescriptions=t pigz=t minid=${params.bbmap_minid}" }
         publishDir = [
             [
                 path: { "${params.outdir}/bbmap/bam" },

nextflow.config

@@ -47,6 +47,7 @@ params {
     // Mapping options
     save_samtools               = false
     save_bam                    = false
+    bbmap_minid                 = 0.9
 
     // orf caller options
     orf_caller                  = 'prodigal'
@@ -290,7 +291,7 @@ manifest {
     description     = """Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0.1'
+    version         = '1.1.0dev'
     doi             = ''
 }
 

nextflow_schema.json

@@ -212,6 +212,13 @@
                 "save_samtools": {
                     "type": "boolean",
                     "description": "Save the output from samtools"
+                },
+                "bbmap_minid": {
+                    "type": "number",
+                    "default": 0.9,
+                    "fa_icon": "fas fa-address-card",
+                    "description": "Minimum identity needed to assign read to a contig",
+                    "help_text": ""
                 }
             },
             "fa_icon": "fas fa-filter"