Merge pull request #872 from d4straub/strict-nextflow

Update to nextflow strict syntax

Author: d4straub

CHANGELOG.md

@@ -21,7 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#876](https://github.com/nf-core/ampliseq/pull/876) Pulled the updated vsearch/clusters module from nf-core to fix a bug where a wildcard expansion trigging an arguments-too-long error.
+- [#872](https://github.com/nf-core/ampliseq/pull/872) - Follow nextflow's strict syntax
+- [#876](https://github.com/nf-core/ampliseq/pull/876) - Pulled the updated vsearch/clusters module from nf-core to fix a bug where a wildcard expansion trigging an arguments-too-long error.
 
 ### `Dependencies`
 

modules.json

@@ -99,7 +99,7 @@
                     },
                     "vsearch/usearchglobal": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "087a2003d9709be9cd580b432a799805777794be",
                         "installed_by": ["modules"]
                     }
                 }

modules/local/assignsh.nf

@@ -17,8 +17,6 @@ process ASSIGNSH {
     path outtable        , emit: tsv
     path "versions.yml"  , emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''

modules/local/barrnap.nf

@@ -15,8 +15,6 @@ process BARRNAP {
     path( "rrna.*.gff" )    , emit: gff
     path "versions.yml"     , emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''

modules/local/barrnapsummary.nf

@@ -14,8 +14,6 @@ process BARRNAPSUMMARY {
     path "*warning.txt", emit: warning
     path "versions.yml", emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''

modules/local/combine_table.nf

@@ -16,8 +16,6 @@ process COMBINE_TABLE {
     path("${outfile}")  , emit: tsv
     path "versions.yml" , emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     """

modules/local/cutadapt_summary.nf

@@ -15,8 +15,6 @@ process CUTADAPT_SUMMARY {
     path("*_summary.tsv") , emit: tsv
     path "versions.yml"   , emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def mode  = meta.single_end ? "single_end" : "paired_end"

modules/local/cutadapt_summary_merge.nf

@@ -15,8 +15,6 @@ process CUTADAPT_SUMMARY_MERGE {
     path("cutadapt_summary.tsv")      , emit: tsv
     path "versions.yml", optional:true, emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     if (action == "merge") {

modules/local/dada2_addspecies.nf

@@ -18,8 +18,6 @@ process DADA2_ADDSPECIES {
     path "versions.yml" , emit: versions
     path "*.args.txt"   , emit: args
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''

modules/local/dada2_denoising.nf

@@ -19,8 +19,6 @@ process DADA2_DENOISING {
     path "versions.yml"                   , emit: versions
     path "*.args.txt"                     , emit: args
 
-    when:
-    task.ext.when == null || task.ext.when
 
     script:
     def prefix = task.ext.prefix ?: "prefix"