Merge pull request #230 from drpatelh/updates

Pre-release bug fixes

CHANGELOG.md

@@ -3,13 +3,14 @@
 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).
 
-## [[2.2](https://github.com/nf-core/rnaseq/releases/tag/2.2)] - 2021-07-28
+## [[2.2](https://github.com/nf-core/rnaseq/releases/tag/2.2)] - 2021-07-29
 
 ### Enhancements & fixes
 
 * Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
 * Remove custom content to render Pangolin report in MultiQC as it was officially added as a module in [v1.11](https://github.com/ewels/MultiQC/pull/1458)
 * [[#212](https://github.com/nf-core/viralrecon/issues/212)] - Access to `PYCOQC.out` is undefined
+* [[#229](https://github.com/nf-core/viralrecon/issues/229)] - ARTIC Guppyplex settings for 1200bp ARTIC primers with Nanopore data
 
 ### Software dependencies
 

conf/base.config

@@ -20,22 +20,22 @@ process {
 
     // Process-specific resource requirements
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 2      * task.attempt, 'cpus'   ) }
+        memory = { check_max( 12.GB  * task.attempt, 'memory' ) }
+        time   = { check_max( 4.h    * task.attempt, 'time'   ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 6      * task.attempt, 'cpus'   ) }
+        memory = { check_max( 36.GB  * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h    * task.attempt, 'time'   ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { check_max( 12     * task.attempt, 'cpus'   ) }
+        memory = { check_max( 72.GB  * task.attempt, 'memory' ) }
+        time   = { check_max( 16.h   * task.attempt, 'time'   ) }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 20.h   * task.attempt, 'time'   ) }
     }
     withLabel:process_high_memory {
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }

conf/modules.config

@@ -102,6 +102,7 @@ params {
             publish_dir     = "${params.artic_minion_caller}/pangolin"
         }
         'nanopore_nextclade' {
+            publish_files   = ['csv':'']
             publish_dir     = "${params.artic_minion_caller}/nextclade"
         }
         'nanopore_asciigenome' {
@@ -298,6 +299,7 @@ params {
             publish_dir     = 'variants/ivar/pangolin'
         }
         'illumina_ivar_nextclade' {
+            publish_files   = ['csv':'']
             publish_dir     = 'variants/ivar/nextclade'
         }
         'illumina_ivar_asciigenome' {
@@ -369,6 +371,7 @@ params {
             publish_dir     = 'variants/bcftools/pangolin'
         }
         'illumina_bcftools_nextclade' {
+            publish_files   = ['csv':'']
             publish_dir     = 'variants/bcftools/nextclade'
         }
         'illumina_bcftools_asciigenome' {

modules.json

@@ -82,7 +82,7 @@
                 "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
             },
             "nextclade": {
-                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+                "git_sha": "29c847424034eb04765d7378fb384ad3094a66a6"
             },
             "pangolin": {
                 "git_sha": "e7e30b6da631ce5288151af4e46488ac6d294ff4"

modules/local/multiqc_illumina.nf

@@ -67,11 +67,11 @@ process MULTIQC {
     multiqc_to_custom_csv.py --platform illumina
 
     ## Manually remove files that we don't want in the report
-    if grep -q skip_assembly workflow_summary_mqc.yaml; then
+    if grep -q ">skip_assembly<" workflow_summary_mqc.yaml; then
         rm -f *assembly_metrics_mqc.csv
     fi
 
-    if grep -q skip_variants workflow_summary_mqc.yaml; then
+    if grep -q ">skip_variants<" workflow_summary_mqc.yaml; then
         rm -f *variants_metrics_mqc.csv
     fi
 

modules/nf-core/modules/nextclade/main.nf

@@ -20,35 +20,28 @@ process NEXTCLADE {
 
     input:
     tuple val(meta), path(fasta)
-    val   output_format
 
     output:
-    tuple val(meta), path("${prefix}.csv")       , optional:true, emit: csv
-    tuple val(meta), path("${prefix}.json")      , optional:true, emit: json
-    tuple val(meta), path("${prefix}.tree.json") , optional:true, emit: json_tree
-    tuple val(meta), path("${prefix}.tsv")       , optional:true, emit: tsv
+    tuple val(meta), path("${prefix}.csv")       , emit: csv
+    tuple val(meta), path("${prefix}.json")      , emit: json
+    tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
+    tuple val(meta), path("${prefix}.tsv")       , emit: tsv
     tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
     path "*.version.txt"                         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def format   = output_format
-    if (!(format in ['json', 'csv', 'tsv', 'tree', 'tsv-clades-only'])) {
-        format = 'json'
-    }
-    def extension = format
-    if (format in ['tsv-clades-only']) {
-        extension = '.clades.tsv'
-    } else if (format in ['tree']) {
-        extension = 'tree.json'
-    }
     """
     nextclade \\
         $options.args \\
         --jobs $task.cpus \\
         --input-fasta $fasta \\
-        --output-${format} ${prefix}.${extension}
+        --output-json ${prefix}.json \\
+        --output-csv ${prefix}.csv \\
+        --output-tsv ${prefix}.tsv \\
+        --output-tsv-clades-only ${prefix}.clades.tsv \\
+        --output-tree ${prefix}.tree.json
 
     echo \$(nextclade --version 2>&1) > ${software}.version.txt
     """

modules/nf-core/modules/nextclade/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: None
       tool_dev_url: https://github.com/nextstrain/nextclade
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -23,11 +23,6 @@ input:
       type: file
       description: FASTA file containing one or more consensus sequences
       pattern: "*.{fasta,fa}"
-  - output_format:
-      type: string
-      description: |
-        String for output format supported by nextclade
-        i.e one of 'json', 'csv', 'tsv', 'tree', 'tsv-clades-only'
 
 output:
   - meta:

subworkflows/local/variants_bcftools.nf

@@ -79,7 +79,7 @@ workflow VARIANTS_BCFTOOLS {
         }
 
         if (!params.skip_nextclade) {
-            NEXTCLADE ( ch_consensus, 'csv' )
+            NEXTCLADE ( ch_consensus )
             ch_nextclade_report  = NEXTCLADE.out.csv
             ch_nextclade_version = NEXTCLADE.out.version
         }

subworkflows/local/variants_ivar.nf

@@ -92,7 +92,7 @@ workflow VARIANTS_IVAR {
         }
 
         if (!params.skip_nextclade) {
-            NEXTCLADE ( ch_consensus, 'csv' )
+            NEXTCLADE ( ch_consensus )
             ch_nextclade_report  = NEXTCLADE.out.csv
             ch_nextclade_version = NEXTCLADE.out.version
         }

workflows/nanopore.nf

@@ -92,9 +92,23 @@ def artic_minion_options   = modules['nanopore_artic_minion']
 artic_minion_options.args += params.artic_minion_caller  == 'medaka' ? Utils.joinModuleArgs(['--medaka']) : ''
 artic_minion_options.args += params.artic_minion_aligner == 'bwa'    ? Utils.joinModuleArgs(['--bwa'])    : Utils.joinModuleArgs(['--minimap2'])
 
+def artic_guppyplex_options = modules['nanopore_artic_guppyplex']
+if (params.primer_set_version == 1200) {
+    def args_split = artic_guppyplex_options.args.tokenize()
+    def min_idx    = args_split.indexOf('--min-length')
+    def max_idx    = args_split.indexOf('--max-length')
+    if (min_idx != -1) {
+        args_split[min_idx+1] = '250'
+    }
+    if (max_idx != -1) {
+        args_split[max_idx+1] = '1500'
+    }
+    artic_guppyplex_options.args = args_split.join(' ')
+}
+
 include { PYCOQC                        } from '../modules/nf-core/modules/pycoqc/main'          addParams( options: modules['nanopore_pycoqc']            )
 include { NANOPLOT                      } from '../modules/nf-core/modules/nanoplot/main'        addParams( options: modules['nanopore_nanoplot']          )
-include { ARTIC_GUPPYPLEX               } from '../modules/nf-core/modules/artic/guppyplex/main' addParams( options: modules['nanopore_artic_guppyplex']   )
+include { ARTIC_GUPPYPLEX               } from '../modules/nf-core/modules/artic/guppyplex/main' addParams( options: artic_guppyplex_options               )
 include { ARTIC_MINION                  } from '../modules/nf-core/modules/artic/minion/main'    addParams( options: artic_minion_options                  )
 include { BCFTOOLS_STATS                } from '../modules/nf-core/modules/bcftools/stats/main'  addParams( options: modules['nanopore_bcftools_stats']    )
 include { QUAST                         } from '../modules/nf-core/modules/quast/main'           addParams( options: modules['nanopore_quast']             )
@@ -373,8 +387,7 @@ workflow NANOPORE {
     ch_nextclade_multiqc = Channel.empty()
     if (!params.skip_nextclade) {
         NEXTCLADE (
-            ARTIC_MINION.out.fasta,
-            'csv'
+            ARTIC_MINION.out.fasta
         )
         ch_software_versions = ch_software_versions.mix(NEXTCLADE.out.version.ifEmpty(null))