Merge remote-tracking branch 'upstream/dev' into samplsheet-for-taxpr…

…ofiler

conf/modules.config

@@ -17,11 +17,7 @@ process {
 
     withName: FASTQC_RAW {
         ext.args = '--quiet'
-        publishDir = [
-            path: { "${params.outdir}/QC_shortreads/fastqc" },
-            mode: params.publish_dir_mode,
-            pattern: "*.html"
-        ]
+        publishDir = [path: { "${params.outdir}/QC_shortreads/fastqc" }, mode: params.publish_dir_mode, pattern: "*.html"]
         ext.prefix = { "${meta.id}_run${meta.run}_raw" }
         tag = { "${meta.id}_run${meta.run}_raw" }
     }
@@ -183,7 +179,7 @@ process {
     }
 
     withName: FILTLONG {
-        ext.args   = [
+        ext.args = [
             "--min_length ${params.longreads_min_length}",
             "--keep_percent ${params.longreads_keep_percent}",
             "--trim",
@@ -261,36 +257,21 @@ process {
     }
 
     withName: MEGAHIT {
-        ext.args = params.megahit_options ?: ''
-        publishDir = [
-            path: { "${params.outdir}/Assembly" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename ->
-                filename.equals('versions.yml')
-                    ? null
-                    : filename.indexOf('.contigs.fa.gz') > 0
-                        ? filename
-                        : filename.indexOf('.log') > 0 ? filename : null
-            }
-        ]
+        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}"]
     }
 
-    withName: SPADES {
-        ext.args = params.spades_options ?: ''
-        publishDir = [
-            path: { "${params.outdir}/Assembly/SPAdes" },
-            mode: params.publish_dir_mode,
-            pattern: "*.{fasta.gz,gfa.gz,log}"
-        ]
+    withName: METASPADES {
+        ext.args = params.spades_options ?: '--meta'
+        ext.prefix = { "SPAdes-${meta.id}" }
+        publishDir = [path: { "${params.outdir}/Assembly/SPAdes" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }
 
-    withName: SPADESHYBRID {
-        ext.args = params.spades_options ?: ''
-        publishDir = [
-            path: { "${params.outdir}/Assembly/SPAdesHybrid" },
-            mode: params.publish_dir_mode,
-            pattern: "*.{fasta.gz,gfa.gz,log}"
-        ]
+    withName: METASPADESHYBRID {
+        ext.args = params.spades_options ?: '--meta'
+        ext.prefix = { "SPAdesHybrid-${meta.id}" }
+        publishDir = [path: { "${params.outdir}/Assembly/SPAdesHybrid" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }
 
     withName: QUAST {
@@ -444,49 +425,30 @@ process {
 
     withName: GTDBTK_SUMMARY {
         ext.args = "--extension fa"
-        publishDir = [
-            path: { "${params.outdir}/Taxonomy/GTDB-Tk" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        publishDir = [path: { "${params.outdir}/Taxonomy/GTDB-Tk" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
 
     withName: PROKKA {
         ext.args = "--metagenome"
-        publishDir = [
-            path: { "${params.outdir}/Annotation/Prokka/${meta.assembler}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        publishDir = [path: { "${params.outdir}/Annotation/Prokka/${meta.assembler}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
 
     withName: PRODIGAL {
         ext.args = "-p meta"
-        publishDir = [
-            path: { "${params.outdir}/Annotation/Prodigal/${meta.assembler}/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        ext.prefix = { "${meta.assembler}-${meta.id}_prodigal" }
+        publishDir = [path: { "${params.outdir}/Annotation/Prodigal/${meta.assembler}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
 
     withName: FREEBAYES {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args = "-p ${params.freebayes_ploidy} -q ${params.freebayes_min_basequality} -F ${params.freebayes_minallelefreq}"
-        publishDir = [
-            path: { "${params.outdir}/Ancient_DNA/variant_calling/freebayes" },
-            mode: params.publish_dir_mode,
-            pattern: "*.vcf.gz"
-        ]
+        publishDir = [path: { "${params.outdir}/Ancient_DNA/variant_calling/freebayes" }, mode: params.publish_dir_mode, pattern: "*.vcf.gz"]
     }
 
     withName: BCFTOOLS_VIEW {
         ext.prefix = { "${meta.assembler}-${meta.id}.filtered" }
         ext.args = "-v snps,mnps -i 'QUAL>=${params.bcftools_view_high_variant_quality} || (QUAL>=${params.bcftools_view_medium_variant_quality} && FORMAT/AO>=${params.bcftools_view_minimal_allelesupport})'"
-        publishDir = [
-            path: { "${params.outdir}/Ancient_DNA/variant_calling/filtered" },
-            mode: params.publish_dir_mode,
-            pattern: "*.vcf.gz"
-        ]
+        publishDir = [path: { "${params.outdir}/Ancient_DNA/variant_calling/filtered" }, mode: params.publish_dir_mode, pattern: "*.vcf.gz"]
     }
 
     withName: BCFTOOLS_CONSENSUS {

nextflow.config

@@ -149,6 +149,10 @@ params {
     metaeuk_db                           = null
     save_mmseqs_db                       = false
 
+    // Generate downstream samplesheets
+    generate_downstream_samplesheets = false
+    generate_pipeline_samplesheets   = null
+
     // References
     //genome                     = null // we use --host_genome instead
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
@@ -185,15 +189,7 @@ params {
     config_profile_url         = null
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genome,genomes,igenomes_base,monochromeLogs'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
-    // Generate downstream samplesheets
-    generate_downstream_samplesheets = false
-    generate_pipeline_samplesheets   = null
+    validate_params            = true
 }
 
 // Load base.config by default for all pipelines

nextflow_schema.json

@@ -877,10 +877,7 @@
             "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/generate_samplesheet_options"
-        },
-        {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
             "$ref": "#/$defs/generic_options"
@@ -914,6 +911,9 @@
         },
         {
             "$ref": "#/$defs/ancient_dna_assembly"
+        },
+        {
+            "$ref": "#/$defs/generate_samplesheet_options"
         }
     ]
 }