Merge pull request #349 from nf-core/maxbin-mincontig

Add metaBAT2 mincontig warning

CHANGELOG.md

@@ -13,7 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#345](https://github.com/nf-core/mag/pull/345) Bowtie2 mode changed to global alignment for ancient DNA mode (`--very-sensitive` mode) to prevent soft clipping at the end of reads when running in local mode.
+- [#345](https://github.com/nf-core/mag/pull/345) - Bowtie2 mode changed to global alignment for ancient DNA mode (`--very-sensitive` mode) to prevent soft clipping at the end of reads when running in local mode.
+- [#349](https://github.com/nf-core/mag/pull/349) - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold.
 
 ### `Dependencies`
 

conf/modules.config

@@ -417,7 +417,7 @@ process {
         ]
         ext.prefix = { "${meta.assembler}-MetaBAT2-${meta.id}" }
         ext.args = [
-            "-m ${params.min_contig_size}",
+            params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
             "--unbinned",
             "--seed ${params.metabat_rng_seed}"
         ].join(' ').trim()

workflows/mag.nf

@@ -35,6 +35,9 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
+// Check MetaBAT2 inputs
+if ( !params.skip_metabat2 && params.min_contig_size < 1500 ) log.warn("Specified min. contig size under minimum for MetaBAT2. MetaBAT2 will be run with 1500 (other binners not affected). You supplied: --min_contig_size ${params.min_contig_size}")
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES