Merge pull request #922 from dialvarezs/review-suggestions

Apply #910 review suggestions

Author: dialvarezs

modules/local/metabinner_bins/main.nf

@@ -2,6 +2,7 @@ process METABINNER_BINS {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metabinner:1.4.4--hdfd78af_0' :

modules/local/metabinner_kmer/main.nf

@@ -2,6 +2,7 @@ process METABINNER_KMER {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metabinner:1.4.4--hdfd78af_0' :

modules/local/metabinner_metabinner/main.nf

@@ -2,6 +2,7 @@ process METABINNER_METABINNER {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metabinner:1.4.4--hdfd78af_0' :

modules/local/metabinner_tooshort/main.nf

@@ -2,6 +2,7 @@ process METABINNER_TOOSHORT {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metabinner:1.4.4--hdfd78af_0' :

subworkflows/local/utils_nfcore_mag_pipeline/main.nf

@@ -360,13 +360,6 @@ def validateInputParameters(hybrid) {
         error("[nf-core/mag] ERROR: Both --skip_binqc and --run_<bin_qc_tool_name> are specified! Invalid combination, please specify either --skip_binqc or --run_<bin_qc_tool_name>.")
     }
 
-    // Check if BUSCO parameters combinations are valid
-    if (params.skip_binqc) {
-        if (params.run_busco) {
-            error("[nf-core/mag] ERROR: Both --skip_binqc and --run_busco specified! Invalid combination, please specify either --skip_binqc or --run_busco with --busco_db.")
-        }
-    }
-
     if (!params.skip_binqc && params.run_busco) {
         if (params.busco_db && !params.busco_db_lineage) {
             log.warn('[nf-core/mag]: WARNING: You have supplied a database to --busco_db - BUSCO will run in offline mode. Please note that BUSCO may fail if you have an incomplete database and are running with --busco_db_lineage auto!')