diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf
index d0b04415a73..bd927f1b58b 100644
--- a/modules/nf-core/abacas/main.nf
+++ b/modules/nf-core/abacas/main.nf
@@ -12,7 +12,7 @@ process ABACAS {
     path  fasta
 
     output:
-    tuple val(meta), path('*.abacas*'), emit: results
+    tuple val(meta), path("*.abacas*"), emit: results
     path "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf
index d128d32426d..864adb9fb7b 100644
--- a/modules/nf-core/adapterremoval/main.nf
+++ b/modules/nf-core/adapterremoval/main.nf
@@ -18,7 +18,7 @@ process ADAPTERREMOVAL {
     tuple val(meta), path("${prefix}.collapsed.fastq.gz")            , optional: true, emit: collapsed
     tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz")  , optional: true, emit: collapsed_truncated
     tuple val(meta), path("${prefix}.paired.fastq.gz")               , optional: true, emit: paired_interleaved
-    tuple val(meta), path('*.settings')                              , emit: settings
+    tuple val(meta), path("*.settings")                              , emit: settings
     path "versions.yml"                                              , emit: versions
 
     when:
diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf
index 26108da758d..23644ccfdce 100644
--- a/modules/nf-core/amplify/predict/main.nf
+++ b/modules/nf-core/amplify/predict/main.nf
@@ -13,7 +13,7 @@ process AMPLIFY_PREDICT {
     path(model_dir)
 
     output:
-    tuple val(meta), path('*.tsv'), emit: tsv
+    tuple val(meta), path("*.tsv"), emit: tsv
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf
index f6801d0a3a6..f20fabbbce2 100644
--- a/modules/nf-core/bandage/image/main.nf
+++ b/modules/nf-core/bandage/image/main.nf
@@ -11,8 +11,8 @@ process BANDAGE_IMAGE {
     tuple val(meta), path(gfa)
 
     output:
-    tuple val(meta), path('*.png'), emit: png
-    tuple val(meta), path('*.svg'), emit: svg
+    tuple val(meta), path("*.png"), emit: png
+    tuple val(meta), path("*.svg"), emit: svg
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
index 0edfa95c9c7..8c3aed6072e 100644
--- a/modules/nf-core/bases2fastq/main.nf
+++ b/modules/nf-core/bases2fastq/main.nf
@@ -8,13 +8,13 @@ process BASES2FASTQ {
     tuple val(meta), path(run_manifest), path(run_dir)
 
     output:
-    tuple val(meta), path('output/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
-    tuple val(meta), path('output/Samples/**/*_stats.json') , emit: sample_json
-    tuple val(meta), path('output/*.html')                  , emit: qc_report
-    tuple val(meta), path('output/RunStats.json')           , emit: run_stats
-    tuple val(meta), path('output/RunManifest.json')        , emit: generated_run_manifest
-    tuple val(meta), path('output/Metrics.csv')             , emit: metrics
-    tuple val(meta), path('output/UnassignedSequences.csv') , emit: unassigned
+    tuple val(meta), path("output/Samples/**/*_R*.fastq.gz"), emit: sample_fastq
+    tuple val(meta), path("output/Samples/**/*_stats.json") , emit: sample_json
+    tuple val(meta), path("output/*.html")                  , emit: qc_report
+    tuple val(meta), path("output/RunStats.json")           , emit: run_stats
+    tuple val(meta), path("output/RunManifest.json")        , emit: generated_run_manifest
+    tuple val(meta), path("output/Metrics.csv")             , emit: metrics
+    tuple val(meta), path("output/UnassignedSequences.csv") , emit: unassigned
     path "versions.yml"                                     , emit: versions
 
     when:
diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf
index 00bbdedad0e..4ec3d6536f4 100644
--- a/modules/nf-core/bbmap/bbduk/main.nf
+++ b/modules/nf-core/bbmap/bbduk/main.nf
@@ -12,8 +12,8 @@ process BBMAP_BBDUK {
     path contaminants
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
-    tuple val(meta), path('*.log')     , emit: log
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
     when:
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index 9eb53208c4d..3f2358c26f9 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -17,10 +17,10 @@ process BBMAP_BBSPLIT {
 
     output:
     path "bbsplit"                            , optional:true, emit: index
-    tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
-    tuple val(meta), path('*fastq.gz')        , optional:true, emit: all_fastq
-    tuple val(meta), path('*txt')             , optional:true, emit: stats
-    tuple val(meta), path('*.log')            , optional:true, emit: log
+    tuple val(meta), path("*primary*fastq.gz"), optional:true, emit: primary_fastq
+    tuple val(meta), path("*fastq.gz")        , optional:true, emit: all_fastq
+    tuple val(meta), path("*txt")             , optional:true, emit: stats
+    tuple val(meta), path("*.log")            , optional:true, emit: log
     path "versions.yml"                       , emit: versions
 
     when:
diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf
index fc6a85ad635..1ef0f4f27e4 100644
--- a/modules/nf-core/bbmap/clumpify/main.nf
+++ b/modules/nf-core/bbmap/clumpify/main.nf
@@ -12,8 +12,8 @@ process BBMAP_CLUMPIFY {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
-    tuple val(meta), path('*.log')     , emit: log
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
     when:
diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf
index 4c6af276ceb..128490b0eb1 100644
--- a/modules/nf-core/bbmap/filterbyname/main.nf
+++ b/modules/nf-core/bbmap/filterbyname/main.nf
@@ -15,7 +15,7 @@ process BBMAP_FILTERBYNAME {
 
     output:
     tuple val(meta), path("*.${output_format}"), emit: reads
-    tuple val(meta), path('*.log')             , emit: log
+    tuple val(meta), path("*.log")             , emit: log
     path "versions.yml"                        , emit: versions
 
     when:
diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
index 0e693e1dfa2..f38f43327df 100644
--- a/modules/nf-core/bcftools/consensus/main.nf
+++ b/modules/nf-core/bcftools/consensus/main.nf
@@ -11,7 +11,7 @@ process BCFTOOLS_CONSENSUS {
     tuple val(meta), path(vcf), path(tbi), path(fasta), path(mask)
 
     output:
-    tuple val(meta), path('*.fa'), emit: fasta
+    tuple val(meta), path("*.fa"), emit: fasta
     path  "versions.yml"         , emit: versions
 
     when:
diff --git a/modules/nf-core/bedops/gtf2bed/main.nf b/modules/nf-core/bedops/gtf2bed/main.nf
index 13a37b5cc85..f7db31533c2 100644
--- a/modules/nf-core/bedops/gtf2bed/main.nf
+++ b/modules/nf-core/bedops/gtf2bed/main.nf
@@ -11,7 +11,7 @@ process BEDOPS_GTF2BED {
     tuple val(meta), path(gtf)
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
+    tuple val(meta), path("*.bed"), emit: bed
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf
index 305b8604d31..5ee3372e0b8 100644
--- a/modules/nf-core/bedtools/complement/main.nf
+++ b/modules/nf-core/bedtools/complement/main.nf
@@ -12,7 +12,7 @@ process BEDTOOLS_COMPLEMENT {
     path  sizes
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
+    tuple val(meta), path("*.bed"), emit: bed
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/bedtools/groupby/main.nf b/modules/nf-core/bedtools/groupby/main.nf
index 063e7ba2a26..9c926bd94c4 100644
--- a/modules/nf-core/bedtools/groupby/main.nf
+++ b/modules/nf-core/bedtools/groupby/main.nf
@@ -12,7 +12,7 @@ process BEDTOOLS_GROUPBY {
     val(summary_col)
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
+    tuple val(meta), path("*.bed"), emit: bed
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf
index 5310647de92..c3a906ccb43 100644
--- a/modules/nf-core/bedtools/merge/main.nf
+++ b/modules/nf-core/bedtools/merge/main.nf
@@ -11,7 +11,7 @@ process BEDTOOLS_MERGE {
     tuple val(meta), path(bed)
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
+    tuple val(meta), path("*.bed"), emit: bed
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
index 68b43ba47f8..01d7d9f8c87 100644
--- a/modules/nf-core/blast/blastn/main.nf
+++ b/modules/nf-core/blast/blastn/main.nf
@@ -12,7 +12,7 @@ process BLAST_BLASTN {
     tuple val(meta2), path(db)
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf
index 98134d2fad6..22dbec625a9 100644
--- a/modules/nf-core/blast/tblastn/main.nf
+++ b/modules/nf-core/blast/tblastn/main.nf
@@ -12,7 +12,7 @@ process BLAST_TBLASTN {
     tuple val(meta2), path(db)
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
index e00acce210f..4d1687563f2 100644
--- a/modules/nf-core/bowtie/align/main.nf
+++ b/modules/nf-core/bowtie/align/main.nf
@@ -13,9 +13,9 @@ process BOWTIE_ALIGN {
     val (save_unaligned)
 
     output:
-    tuple val(meta), path('*.bam')     , emit: bam
-    tuple val(meta), path('*.out')     , emit: log
-    tuple val(meta), path('*fastq.gz') , emit: fastq, optional : true
+    tuple val(meta), path("*.bam")     , emit: bam
+    tuple val(meta), path("*.out")     , emit: log
+    tuple val(meta), path("*fastq.gz") , emit: fastq, optional : true
     path  "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf
index 953e12f6875..52b6199a00d 100644
--- a/modules/nf-core/bowtie/build/main.nf
+++ b/modules/nf-core/bowtie/build/main.nf
@@ -11,7 +11,7 @@ process BOWTIE_BUILD {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('bowtie') , emit: index
+    tuple val(meta), path("bowtie") , emit: index
     path "versions.yml"             , emit: versions
 
     when:
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 9e2e0e5e2cc..71fd17faf43 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -11,7 +11,7 @@ process BOWTIE2_BUILD {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('bowtie2')    , emit: index
+    tuple val(meta), path("bowtie2")    , emit: index
     path "versions.yml"                 , emit: versions
 
     when:
diff --git a/modules/nf-core/cellsnp/modea/main.nf b/modules/nf-core/cellsnp/modea/main.nf
index 048a2449225..7c09ca7fab2 100644
--- a/modules/nf-core/cellsnp/modea/main.nf
+++ b/modules/nf-core/cellsnp/modea/main.nf
@@ -11,12 +11,12 @@ process CELLSNP_MODEA {
     tuple val(meta), path(bam), path(bai), path(region_vcf), path(barcode)
 
     output:
-    tuple val(meta), path('*.base.vcf.gz') , emit: base
-    tuple val(meta), path('*.cells.vcf.gz'), emit: cell          , optional: true
-    tuple val(meta), path('*.samples.tsv') , emit: sample
-    tuple val(meta), path('*.tag.AD.mtx')  , emit: allele_depth
-    tuple val(meta), path('*.tag.DP.mtx')  , emit: depth_coverage
-    tuple val(meta), path('*.tag.OTH.mtx') , emit: depth_other
+    tuple val(meta), path("*.base.vcf.gz") , emit: base
+    tuple val(meta), path("*.cells.vcf.gz"), emit: cell          , optional: true
+    tuple val(meta), path("*.samples.tsv") , emit: sample
+    tuple val(meta), path("*.tag.AD.mtx")  , emit: allele_depth
+    tuple val(meta), path("*.tag.DP.mtx")  , emit: depth_coverage
+    tuple val(meta), path("*.tag.OTH.mtx") , emit: depth_other
     path 'versions.yml'                    , emit: versions
 
     when:
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
index d9a5653df56..8e0452f3757 100644
--- a/modules/nf-core/centrifuge/centrifuge/main.nf
+++ b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -14,11 +14,11 @@ process CENTRIFUGE_CENTRIFUGE {
     val save_aligned
 
     output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
+    tuple val(meta), path("*report.txt")                 , emit: report
+    tuple val(meta), path("*results.txt")                , emit: results
+    tuple val(meta), path("*.{sam,tab}")                 , optional: true, emit: sam
+    tuple val(meta), path("*.mapped.fastq{,.1,.2}.gz")   , optional: true, emit: fastq_mapped
+    tuple val(meta), path("*.unmapped.fastq{,.1,.2}.gz") , optional: true, emit: fastq_unmapped
     path "versions.yml"                                  , emit: versions
 
     when:
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
index 25eb7167b7c..1e4b2f601cd 100644
--- a/modules/nf-core/centrifuge/kreport/main.nf
+++ b/modules/nf-core/centrifuge/kreport/main.nf
@@ -12,7 +12,7 @@ process CENTRIFUGE_KREPORT {
     path db
 
     output:
-    tuple val(meta), path('*.txt'), emit: kreport
+    tuple val(meta), path("*.txt"), emit: kreport
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index 577117ed443..c359a3316b2 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -11,7 +11,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
     val ids
 
     output:
-    path('*.mkfg')     , emit: ncbi_settings
+    path("*.mkfg")     , emit: ncbi_settings
     path 'versions.yml', emit: versions
 
     when:
diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf
index 3d3e571689c..6ee775204ed 100644
--- a/modules/nf-core/cutadapt/main.nf
+++ b/modules/nf-core/cutadapt/main.nf
@@ -11,8 +11,8 @@ process CUTADAPT {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.trim.fastq.gz'), emit: reads
-    tuple val(meta), path('*.log')          , emit: log
+    tuple val(meta), path("*.trim.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")          , emit: log
     path "versions.yml"                     , emit: versions
 
     when:
diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf
index dc01cdcc08c..7751367cd1a 100644
--- a/modules/nf-core/diamond/blastp/main.nf
+++ b/modules/nf-core/diamond/blastp/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTP {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.blast'), optional: true, emit: blast
-    tuple val(meta), path('*.xml')  , optional: true, emit: xml
-    tuple val(meta), path('*.txt')  , optional: true, emit: txt
-    tuple val(meta), path('*.daa')  , optional: true, emit: daa
-    tuple val(meta), path('*.sam')  , optional: true, emit: sam
-    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
-    tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    tuple val(meta), path("*.blast"), optional: true, emit: blast
+    tuple val(meta), path("*.xml")  , optional: true, emit: xml
+    tuple val(meta), path("*.txt")  , optional: true, emit: txt
+    tuple val(meta), path("*.daa")  , optional: true, emit: daa
+    tuple val(meta), path("*.sam")  , optional: true, emit: sam
+    tuple val(meta), path("*.tsv")  , optional: true, emit: tsv
+    tuple val(meta), path("*.paf")  , optional: true, emit: paf
     path "versions.yml"             , emit: versions
 
     when:
diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf
index bf3f623c74c..fa5387cc53a 100644
--- a/modules/nf-core/diamond/blastx/main.nf
+++ b/modules/nf-core/diamond/blastx/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTX {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.blast'), optional: true, emit: blast
-    tuple val(meta), path('*.xml')  , optional: true, emit: xml
-    tuple val(meta), path('*.txt')  , optional: true, emit: txt
-    tuple val(meta), path('*.daa')  , optional: true, emit: daa
-    tuple val(meta), path('*.sam')  , optional: true, emit: sam
-    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
-    tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    tuple val(meta), path("*.blast"), optional: true, emit: blast
+    tuple val(meta), path("*.xml")  , optional: true, emit: xml
+    tuple val(meta), path("*.txt")  , optional: true, emit: txt
+    tuple val(meta), path("*.daa")  , optional: true, emit: daa
+    tuple val(meta), path("*.sam")  , optional: true, emit: sam
+    tuple val(meta), path("*.tsv")  , optional: true, emit: tsv
+    tuple val(meta), path("*.paf")  , optional: true, emit: paf
     tuple val(meta), path("*.log")  , emit: log
     path "versions.yml"             , emit: versions
 
diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf
index 760c2dfbad0..2ae3a4513e0 100644
--- a/modules/nf-core/dragmap/align/main.nf
+++ b/modules/nf-core/dragmap/align/main.nf
@@ -19,7 +19,7 @@ process DRAGMAP_ALIGN {
     tuple val(meta), path("*.cram") , emit: cram  , optional: true
     tuple val(meta), path("*.crai") , emit: crai  , optional: true
     tuple val(meta), path("*.csi")  , emit: csi   , optional: true
-    tuple val(meta), path('*.log')  , emit: log
+    tuple val(meta), path("*.log")  , emit: log
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/dysgu/main.nf b/modules/nf-core/dysgu/main.nf
index 6aa1deea958..035348f1138 100644
--- a/modules/nf-core/dysgu/main.nf
+++ b/modules/nf-core/dysgu/main.nf
@@ -12,8 +12,8 @@ process DYSGU {
     tuple val(meta2), path(fasta), path(fai)
 
     output:
-    tuple val(meta), path('*.vcf.gz')       , emit: vcf
-    tuple val(meta), path('*.vcf.gz.tbi')   , emit: tbi
+    tuple val(meta), path("*.vcf.gz")       , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi")   , emit: tbi
     path 'versions.yml'                     , emit: versions
 
     when:
diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf
index 7560a55e4cb..cfa4a3ee52d 100644
--- a/modules/nf-core/faqcs/main.nf
+++ b/modules/nf-core/faqcs/main.nf
@@ -11,13 +11,13 @@ process FAQCS {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.trimmed.fastq.gz')           , emit: reads         , optional: true
-    tuple val(meta), path('*.stats.txt')                  , emit: stats         , optional: true
-    tuple val(meta), path('./debug')                      , emit: debug         , optional: true
-    tuple val(meta), path('*_qc_report.pdf')              , emit: statspdf      , optional: true
-    tuple val(meta), path('*.discard.fastq.gz')           , emit: reads_fail    , optional: true
-    tuple val(meta), path('*.trimmed.unpaired.fastq.gz')  , emit: reads_unpaired, optional: true
-    tuple val(meta), path('*.log')                        , emit: log
+    tuple val(meta), path("*.trimmed.fastq.gz")           , emit: reads         , optional: true
+    tuple val(meta), path("*.stats.txt")                  , emit: stats         , optional: true
+    tuple val(meta), path("./debug")                      , emit: debug         , optional: true
+    tuple val(meta), path("*_qc_report.pdf")              , emit: statspdf      , optional: true
+    tuple val(meta), path("*.discard.fastq.gz")           , emit: reads_fail    , optional: true
+    tuple val(meta), path("*.trimmed.unpaired.fastq.gz")  , emit: reads_unpaired, optional: true
+    tuple val(meta), path("*.log")                        , emit: log
     path "versions.yml"                                   , emit: versions
 
     when:
diff --git a/modules/nf-core/fastavalidator/main.nf b/modules/nf-core/fastavalidator/main.nf
index ac5470fb6d4..a4596006cc5 100644
--- a/modules/nf-core/fastavalidator/main.nf
+++ b/modules/nf-core/fastavalidator/main.nf
@@ -11,8 +11,8 @@ process FASTAVALIDATOR {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('*.success.log')  , emit: success_log , optional: true
-    tuple val(meta), path('*.error.log')    , emit: error_log   , optional: true
+    tuple val(meta), path("*.success.log")  , emit: success_log , optional: true
+    tuple val(meta), path("*.error.log")    , emit: error_log   , optional: true
     path "versions.yml"                     , emit: versions
 
     when:
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index e1b9f565609..19f71d420e7 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -15,12 +15,12 @@ process FASTP {
     val   save_merged
 
     output:
-    tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
-    tuple val(meta), path('*.json')           , emit: json
-    tuple val(meta), path('*.html')           , emit: html
-    tuple val(meta), path('*.log')            , emit: log
-    tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
-    tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
+    tuple val(meta), path("*.fastp.fastq.gz") , optional:true, emit: reads
+    tuple val(meta), path("*.json")           , emit: json
+    tuple val(meta), path("*.html")           , emit: html
+    tuple val(meta), path("*.log")            , emit: log
+    tuple val(meta), path("*.fail.fastq.gz")  , optional:true, emit: reads_fail
+    tuple val(meta), path("*.merged.fastq.gz"), optional:true, emit: reads_merged
     path "versions.yml"                       , emit: versions
 
     when:
diff --git a/modules/nf-core/fqtk/main.nf b/modules/nf-core/fqtk/main.nf
index 30e1b22afd5..8c079da9eb8 100644
--- a/modules/nf-core/fqtk/main.nf
+++ b/modules/nf-core/fqtk/main.nf
@@ -14,9 +14,9 @@ process FQTK {
 
     output:
     // Demultiplexed file name changes depending on the arg '--output-types'
-    tuple val(meta), path('output/*.fq.gz')                         , emit: sample_fastq
-    tuple val(meta), path('output/demux-metrics.txt')               , emit: metrics
-    tuple val(meta), path('output/unmatched*.fq.gz')                , emit: most_frequent_unmatched
+    tuple val(meta), path("output/*.fq.gz")                         , emit: sample_fastq
+    tuple val(meta), path("output/demux-metrics.txt")               , emit: metrics
+    tuple val(meta), path("output/unmatched*.fq.gz")                , emit: most_frequent_unmatched
     path "versions.yml"                                             , emit: versions
 
 
diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf
index 89960e04cac..627c7c47eff 100644
--- a/modules/nf-core/gatk4/bedtointervallist/main.nf
+++ b/modules/nf-core/gatk4/bedtointervallist/main.nf
@@ -12,7 +12,7 @@ process GATK4_BEDTOINTERVALLIST {
     tuple val(meta2), path(dict)
 
     output:
-    tuple val(meta), path('*.interval_list'), emit: interval_list
+    tuple val(meta), path("*.interval_list"), emit: interval_list
     path  "versions.yml"                    , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf
index 20fe3c5e139..e0204671b4a 100644
--- a/modules/nf-core/gatk4/calculatecontamination/main.nf
+++ b/modules/nf-core/gatk4/calculatecontamination/main.nf
@@ -11,8 +11,8 @@ process GATK4_CALCULATECONTAMINATION {
     tuple val(meta), path(pileup), path(matched)
 
     output:
-    tuple val(meta), path('*.contamination.table'), emit: contamination
-    tuple val(meta), path('*.segmentation.table') , emit: segmentation, optional:true
+    tuple val(meta), path("*.contamination.table"), emit: contamination
+    tuple val(meta), path("*.segmentation.table") , emit: segmentation, optional:true
     path "versions.yml"                           , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
index 998622a0658..05496734219 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -11,7 +11,7 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('*.dict')  , emit: dict
+    tuple val(meta), path("*.dict")  , emit: dict
     path "versions.yml"              , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
index 9071279577f..f091bfba44e 100644
--- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
+++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
@@ -14,7 +14,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     path  dict
 
     output:
-    tuple val(meta), path('*.metrics'), emit: metrics
+    tuple val(meta), path("*.metrics"), emit: metrics
     path "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf
index 41fd3128118..4f1bf0b83bd 100644
--- a/modules/nf-core/gatk4/getpileupsummaries/main.nf
+++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf
@@ -16,7 +16,7 @@ process GATK4_GETPILEUPSUMMARIES {
     path  variants_tbi
 
     output:
-    tuple val(meta), path('*.pileups.table'), emit: table
+    tuple val(meta), path("*.pileups.table"), emit: table
     path "versions.yml"                     , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf
index 69027e05305..4778fc981f5 100644
--- a/modules/nf-core/gatk4/mergebamalignment/main.nf
+++ b/modules/nf-core/gatk4/mergebamalignment/main.nf
@@ -13,7 +13,7 @@ process GATK4_MERGEBAMALIGNMENT {
     tuple val(meta3), path(dict)
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf
index 1752f48a604..a13b20b962d 100644
--- a/modules/nf-core/gatk4/mergevcfs/main.nf
+++ b/modules/nf-core/gatk4/mergevcfs/main.nf
@@ -12,7 +12,7 @@ process GATK4_MERGEVCFS {
     tuple val(meta2), path(dict)
 
     output:
-    tuple val(meta), path('*.vcf.gz'), emit: vcf
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
     tuple val(meta), path("*.tbi")   , emit: tbi
     path  "versions.yml"             , emit: versions
 
diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf
index ad2d38ab446..2abcb14bc9e 100644
--- a/modules/nf-core/gatk4/revertsam/main.nf
+++ b/modules/nf-core/gatk4/revertsam/main.nf
@@ -11,7 +11,7 @@ process GATK4_REVERTSAM {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf
index 7760d4581bf..6ee948fb90b 100644
--- a/modules/nf-core/gatk4/samtofastq/main.nf
+++ b/modules/nf-core/gatk4/samtofastq/main.nf
@@ -11,7 +11,7 @@ process GATK4_SAMTOFASTQ {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: fastq
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
     path  "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf
index 40bfee1b30a..981be17b349 100644
--- a/modules/nf-core/gatk4/splitncigarreads/main.nf
+++ b/modules/nf-core/gatk4/splitncigarreads/main.nf
@@ -14,7 +14,7 @@ process GATK4_SPLITNCIGARREADS {
     tuple val(meta4), path(dict)
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/gt/gff3validator/main.nf b/modules/nf-core/gt/gff3validator/main.nf
index 8c6899cafa3..5a1bd7e3bc3 100644
--- a/modules/nf-core/gt/gff3validator/main.nf
+++ b/modules/nf-core/gt/gff3validator/main.nf
@@ -11,8 +11,8 @@ process GT_GFF3VALIDATOR {
     tuple val(meta), path(gff3)
 
     output:
-    tuple val(meta), path('*.success.log')  , emit: success_log , optional: true
-    tuple val(meta), path('*.error.log')    , emit: error_log   , optional: true
+    tuple val(meta), path("*.success.log")  , emit: success_log , optional: true
+    tuple val(meta), path("*.error.log")    , emit: error_log   , optional: true
     path "versions.yml"                     , emit: versions
 
     when:
diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf
index a883ce22537..7d4dc8d05dd 100644
--- a/modules/nf-core/happy/happy/main.nf
+++ b/modules/nf-core/happy/happy/main.nf
@@ -17,17 +17,17 @@ process HAPPY_HAPPY {
     tuple val(meta6), path(stratification_beds)
 
     output:
-    tuple val(meta), path('*.summary.csv')                      , emit: summary_csv
-    tuple val(meta), path('*.roc.all.csv.gz')                   , emit: roc_all_csv
-    tuple val(meta), path('*.roc.Locations.INDEL.csv.gz')       , emit: roc_indel_locations_csv
-    tuple val(meta), path('*.roc.Locations.INDEL.PASS.csv.gz')  , emit: roc_indel_locations_pass_csv
-    tuple val(meta), path('*.roc.Locations.SNP.csv.gz')         , emit: roc_snp_locations_csv
-    tuple val(meta), path('*.roc.Locations.SNP.PASS.csv.gz')    , emit: roc_snp_locations_pass_csv
-    tuple val(meta), path('*.extended.csv')                     , emit: extended_csv
-    tuple val(meta), path('*.runinfo.json')                     , emit: runinfo
-    tuple val(meta), path('*.metrics.json.gz')                  , emit: metrics_json
-    tuple val(meta), path('*.vcf.gz')                           , emit: vcf, optional:true
-    tuple val(meta), path('*.tbi')                              , emit: tbi, optional:true
+    tuple val(meta), path("*.summary.csv")                      , emit: summary_csv
+    tuple val(meta), path("*.roc.all.csv.gz")                   , emit: roc_all_csv
+    tuple val(meta), path("*.roc.Locations.INDEL.csv.gz")       , emit: roc_indel_locations_csv
+    tuple val(meta), path("*.roc.Locations.INDEL.PASS.csv.gz")  , emit: roc_indel_locations_pass_csv
+    tuple val(meta), path("*.roc.Locations.SNP.csv.gz")         , emit: roc_snp_locations_csv
+    tuple val(meta), path("*.roc.Locations.SNP.PASS.csv.gz")    , emit: roc_snp_locations_pass_csv
+    tuple val(meta), path("*.extended.csv")                     , emit: extended_csv
+    tuple val(meta), path("*.runinfo.json")                     , emit: runinfo
+    tuple val(meta), path("*.metrics.json.gz")                  , emit: metrics_json
+    tuple val(meta), path("*.vcf.gz")                           , emit: vcf, optional:true
+    tuple val(meta), path("*.tbi")                              , emit: tbi, optional:true
     path "versions.yml"                                         , emit: versions
 
     when:
diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf
index 57333acf79d..75fc407e5b3 100644
--- a/modules/nf-core/happy/prepy/main.nf
+++ b/modules/nf-core/happy/prepy/main.nf
@@ -14,7 +14,7 @@ process HAPPY_PREPY {
     tuple val(meta3), path(fasta_fai)
 
     output:
-    tuple val(meta), path('*.vcf.gz')  , emit: preprocessed_vcf
+    tuple val(meta), path("*.vcf.gz")  , emit: preprocessed_vcf
     path "versions.yml"                , emit: versions
 
     when:
diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf
index ba23fd16765..ef4235c98fe 100644
--- a/modules/nf-core/happy/sompy/main.nf
+++ b/modules/nf-core/happy/sompy/main.nf
@@ -17,9 +17,9 @@ process HAPPY_SOMPY {
     tuple val(meta6), path(bams)
 
     output:
-    tuple val(meta), path('*.features.csv')           , emit: features, optional: true
-    tuple val(meta), path('*.metrics.json')           , emit: metrics
-    tuple val(meta), path('*.stats.csv')              , emit: stats
+    tuple val(meta), path("*.features.csv")           , emit: features, optional: true
+    tuple val(meta), path("*.metrics.json")           , emit: metrics
+    tuple val(meta), path("*.stats.csv")              , emit: stats
     path "versions.yml"                               , emit: versions
 
     when:
diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf
index 603a865e85f..bad664cfa4d 100644
--- a/modules/nf-core/hmmer/hmmsearch/main.nf
+++ b/modules/nf-core/hmmer/hmmsearch/main.nf
@@ -11,10 +11,10 @@ process HMMER_HMMSEARCH {
     tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain)
 
     output:
-    tuple val(meta), path('*.txt.gz')   , emit: output
-    tuple val(meta), path('*.sto.gz')   , emit: alignments    , optional: true
-    tuple val(meta), path('*.tbl.gz')   , emit: target_summary, optional: true
-    tuple val(meta), path('*.domtbl.gz'), emit: domain_summary, optional: true
+    tuple val(meta), path("*.txt.gz")   , emit: output
+    tuple val(meta), path("*.sto.gz")   , emit: alignments    , optional: true
+    tuple val(meta), path("*.tbl.gz")   , emit: target_summary, optional: true
+    tuple val(meta), path("*.domtbl.gz"), emit: domain_summary, optional: true
     path "versions.yml"                 , emit: versions
 
     when:
diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf
index add9b031747..40dfa3175f4 100644
--- a/modules/nf-core/interproscan/main.nf
+++ b/modules/nf-core/interproscan/main.nf
@@ -13,10 +13,10 @@ process INTERPROSCAN {
     path(interproscan_database, stageAs: 'data')
 
     output:
-    tuple val(meta), path('*.tsv') , optional: true, emit: tsv
-    tuple val(meta), path('*.xml') , optional: true, emit: xml
-    tuple val(meta), path('*.gff3'), optional: true, emit: gff3
-    tuple val(meta), path('*.json'), optional: true, emit: json
+    tuple val(meta), path("*.tsv") , optional: true, emit: tsv
+    tuple val(meta), path("*.xml") , optional: true, emit: xml
+    tuple val(meta), path("*.gff3"), optional: true, emit: gff3
+    tuple val(meta), path("*.json"), optional: true, emit: json
     path "versions.yml"            , emit: versions
 
     when:
diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf
index 5348deeeb08..b8052cdcdc4 100644
--- a/modules/nf-core/ivar/trim/main.nf
+++ b/modules/nf-core/ivar/trim/main.nf
@@ -13,7 +13,7 @@ process IVAR_TRIM {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path('*.log'), emit: log
+    tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf
index 2f5f6e7d8c9..85d5b3764ef 100644
--- a/modules/nf-core/kaiju/kaiju/main.nf
+++ b/modules/nf-core/kaiju/kaiju/main.nf
@@ -12,7 +12,7 @@ process KAIJU_KAIJU {
     path(db)
 
     output:
-    tuple val(meta), path('*.tsv'), emit: results
+    tuple val(meta), path("*.tsv"), emit: results
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf
index 44049744ada..1869101a075 100644
--- a/modules/nf-core/kaiju/kaiju2table/main.nf
+++ b/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -13,7 +13,7 @@ process KAIJU_KAIJU2TABLE {
     val taxon_rank
 
     output:
-    tuple val(meta), path('*.txt'), emit: summary
+    tuple val(meta), path("*.txt"), emit: summary
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/kofamscan/main.nf b/modules/nf-core/kofamscan/main.nf
index 0a2e5d66312..da1d5df16a7 100644
--- a/modules/nf-core/kofamscan/main.nf
+++ b/modules/nf-core/kofamscan/main.nf
@@ -13,8 +13,8 @@ process KOFAMSCAN {
     path ko_list
 
     output:
-    tuple val(meta), path('*.txt'), optional: true, emit: txt
-    tuple val(meta), path('*.tsv'), optional: true, emit: tsv
+    tuple val(meta), path("*.txt"), optional: true, emit: txt
+    tuple val(meta), path("*.tsv"), optional: true, emit: tsv
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf
index 364a6fe2493..c62f050e200 100644
--- a/modules/nf-core/kraken2/kraken2/main.nf
+++ b/modules/nf-core/kraken2/kraken2/main.nf
@@ -14,10 +14,10 @@ process KRAKEN2_KRAKEN2 {
     val save_reads_assignment
 
     output:
-    tuple val(meta), path('*.classified{.,_}*')     , optional:true, emit: classified_reads_fastq
-    tuple val(meta), path('*.unclassified{.,_}*')   , optional:true, emit: unclassified_reads_fastq
-    tuple val(meta), path('*classifiedreads.txt')   , optional:true, emit: classified_reads_assignment
-    tuple val(meta), path('*report.txt')                           , emit: report
+    tuple val(meta), path("*.classified{.,_}*")     , optional:true, emit: classified_reads_fastq
+    tuple val(meta), path("*.unclassified{.,_}*")   , optional:true, emit: unclassified_reads_fastq
+    tuple val(meta), path("*classifiedreads.txt")   , optional:true, emit: classified_reads_assignment
+    tuple val(meta), path("*report.txt")                           , emit: report
     path "versions.yml"                                            , emit: versions
 
     when:
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
index 3a31fcb40fe..8aac7493d7e 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
@@ -20,8 +20,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     output:
     tuple val(meta), path("*.classified.${sequence_type}.gz")  , optional:true, emit: classified_reads
     tuple val(meta), path("*.unclassified.${sequence_type}.gz"), optional:true, emit: unclassified_reads
-    tuple val(meta), path('*.krakenuniq.classified.txt')       , optional:true, emit: classified_assignment
-    tuple val(meta), path('*.krakenuniq.report.txt')           , emit: report
+    tuple val(meta), path("*.krakenuniq.classified.txt")       , optional:true, emit: classified_assignment
+    tuple val(meta), path("*.krakenuniq.report.txt")           , emit: report
     path "versions.yml"                                        , emit: versions
 
     when:
diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf
index db0612422bd..81f653aacb3 100644
--- a/modules/nf-core/megahit/main.nf
+++ b/modules/nf-core/megahit/main.nf
@@ -15,7 +15,7 @@ process MEGAHIT {
     tuple val(meta), path("intermediate_contigs/k*.addi.fa.gz")         , emit: addi_contigs
     tuple val(meta), path("intermediate_contigs/k*.local.fa.gz")        , emit: local_contigs
     tuple val(meta), path("intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs
-    tuple val(meta), path('*.log')                                      , emit: log
+    tuple val(meta), path("*.log")                                      , emit: log
     path "versions.yml"                                                 , emit: versions
 
     when:
diff --git a/modules/nf-core/merqury/hapmers/main.nf b/modules/nf-core/merqury/hapmers/main.nf
index 22dd66d5f6a..3d161ad911a 100644
--- a/modules/nf-core/merqury/hapmers/main.nf
+++ b/modules/nf-core/merqury/hapmers/main.nf
@@ -13,11 +13,11 @@ process MERQURY_HAPMERS {
     path(paternal_meryl, stageAs: 'pat.meryl')
 
     output:
-    tuple val(meta), path('*_mat.hapmer.meryl')         , emit: mat_hapmer_meryl
-    tuple val(meta), path('*_pat.hapmer.meryl')         , emit: pat_hapmer_meryl
-    tuple val(meta), path('*_inherited_hapmers.fl.png') , emit: inherited_hapmers_fl_png
-    tuple val(meta), path('*_inherited_hapmers.ln.png') , emit: inherited_hapmers_ln_png
-    tuple val(meta), path('*_inherited_hapmers.st.png') , emit: inherited_hapmers_st_png
+    tuple val(meta), path("*_mat.hapmer.meryl")         , emit: mat_hapmer_meryl
+    tuple val(meta), path("*_pat.hapmer.meryl")         , emit: pat_hapmer_meryl
+    tuple val(meta), path("*_inherited_hapmers.fl.png") , emit: inherited_hapmers_fl_png
+    tuple val(meta), path("*_inherited_hapmers.ln.png") , emit: inherited_hapmers_ln_png
+    tuple val(meta), path("*_inherited_hapmers.st.png") , emit: inherited_hapmers_st_png
     path "versions.yml"                                 , emit: versions
 
     when:
diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf
index c427efebbdb..fcfb1bb3784 100644
--- a/modules/nf-core/metaphlan/metaphlan/main.nf
+++ b/modules/nf-core/metaphlan/metaphlan/main.nf
@@ -14,7 +14,7 @@ process METAPHLAN_METAPHLAN {
     output:
     tuple val(meta), path("*_profile.txt")   ,                emit: profile
     tuple val(meta), path("*.biom")          ,                emit: biom
-    tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
+    tuple val(meta), path("*.bowtie2out.txt"), optional:true, emit: bt2out
     path "versions.yml"                      ,                emit: versions
 
     when:
diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf
index 53cd7f9836b..e94d8148fad 100644
--- a/modules/nf-core/metaphlan3/metaphlan3/main.nf
+++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf
@@ -14,7 +14,7 @@ process METAPHLAN3_METAPHLAN3 {
     output:
     tuple val(meta), path("*_profile.txt")   ,                emit: profile
     tuple val(meta), path("*.biom")          ,                emit: biom
-    tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
+    tuple val(meta), path("*.bowtie2out.txt"), optional:true, emit: bt2out
     path "versions.yml"                      ,                emit: versions
 
     when:
diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf
index 55ff6062132..ce792751519 100644
--- a/modules/nf-core/minia/main.nf
+++ b/modules/nf-core/minia/main.nf
@@ -11,9 +11,9 @@ process MINIA {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.contigs.fa'), emit: contigs
-    tuple val(meta), path('*.unitigs.fa'), emit: unitigs
-    tuple val(meta), path('*.h5')        , emit: h5
+    tuple val(meta), path("*.contigs.fa"), emit: contigs
+    tuple val(meta), path("*.unitigs.fa"), emit: unitigs
+    tuple val(meta), path("*.h5")        , emit: h5
     path  "versions.yml"                 , emit: versions
 
     when:
diff --git a/modules/nf-core/mirdeep2/mapper/main.nf b/modules/nf-core/mirdeep2/mapper/main.nf
index d52820a362b..aca4b780e15 100644
--- a/modules/nf-core/mirdeep2/mapper/main.nf
+++ b/modules/nf-core/mirdeep2/mapper/main.nf
@@ -12,7 +12,7 @@ process MIRDEEP2_MAPPER {
     tuple val(meta2), path(index, stageAs: '*')
 
     output:
-    tuple val(meta), path('*.fa'), path('*.arf'), emit: outputs
+    tuple val(meta), path("*.fa"), path("*.arf"), emit: outputs
     path "versions.yml"                         , emit: versions
 
     when:
diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
index 6f4a838343c..36eb4854c74 100644
--- a/modules/nf-core/mosdepth/main.nf
+++ b/modules/nf-core/mosdepth/main.nf
@@ -12,18 +12,18 @@ process MOSDEPTH {
     tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path('*.global.dist.txt')      , emit: global_txt
-    tuple val(meta), path('*.summary.txt')          , emit: summary_txt
-    tuple val(meta), path('*.region.dist.txt')      , optional:true, emit: regions_txt
-    tuple val(meta), path('*.per-base.d4')          , optional:true, emit: per_base_d4
-    tuple val(meta), path('*.per-base.bed.gz')      , optional:true, emit: per_base_bed
-    tuple val(meta), path('*.per-base.bed.gz.csi')  , optional:true, emit: per_base_csi
-    tuple val(meta), path('*.regions.bed.gz')       , optional:true, emit: regions_bed
-    tuple val(meta), path('*.regions.bed.gz.csi')   , optional:true, emit: regions_csi
-    tuple val(meta), path('*.quantized.bed.gz')     , optional:true, emit: quantized_bed
-    tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
-    tuple val(meta), path('*.thresholds.bed.gz')    , optional:true, emit: thresholds_bed
-    tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
+    tuple val(meta), path("*.global.dist.txt")      , emit: global_txt
+    tuple val(meta), path("*.summary.txt")          , emit: summary_txt
+    tuple val(meta), path("*.region.dist.txt")      , optional:true, emit: regions_txt
+    tuple val(meta), path("*.per-base.d4")          , optional:true, emit: per_base_d4
+    tuple val(meta), path("*.per-base.bed.gz")      , optional:true, emit: per_base_bed
+    tuple val(meta), path("*.per-base.bed.gz.csi")  , optional:true, emit: per_base_csi
+    tuple val(meta), path("*.regions.bed.gz")       , optional:true, emit: regions_bed
+    tuple val(meta), path("*.regions.bed.gz.csi")   , optional:true, emit: regions_csi
+    tuple val(meta), path("*.quantized.bed.gz")     , optional:true, emit: quantized_bed
+    tuple val(meta), path("*.quantized.bed.gz.csi") , optional:true, emit: quantized_csi
+    tuple val(meta), path("*.thresholds.bed.gz")    , optional:true, emit: thresholds_bed
+    tuple val(meta), path("*.thresholds.bed.gz.csi"), optional:true, emit: thresholds_csi
     path  "versions.yml"                            , emit: versions
 
     when:
diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf
index f3a91a8a877..b9eced2dfa9 100644
--- a/modules/nf-core/multivcfanalyzer/main.nf
+++ b/modules/nf-core/multivcfanalyzer/main.nf
@@ -21,17 +21,17 @@ process MULTIVCFANALYZER {
 
 
     output:
-    tuple val(meta), path('fullAlignment.fasta.gz')                       , emit: full_alignment
-    tuple val(meta), path('info.txt')                                     , emit: info_txt
-    tuple val(meta), path('snpAlignment.fasta.gz')                        , emit: snp_alignment
-    tuple val(meta), path('snpAlignmentIncludingRefGenome.fasta.gz')      , emit: snp_genome_alignment
-    tuple val(meta), path('snpStatistics.tsv')                            , emit: snpstatistics
-    tuple val(meta), path('snpTable.tsv')                                 , emit: snptable
-    tuple val(meta), path('snpTableForSnpEff.tsv')                        , emit: snptable_snpeff
-    tuple val(meta), path('snpTableWithUncertaintyCalls.tsv')             , emit: snptable_uncertainty
-    tuple val(meta), path('structureGenotypes.tsv')                       , emit: structure_genotypes
-    tuple val(meta), path('structureGenotypes_noMissingData-Columns.tsv') , emit: structure_genotypes_nomissing
-    tuple val(meta), path('MultiVCFAnalyzer.json')                        , emit: json
+    tuple val(meta), path("fullAlignment.fasta.gz")                       , emit: full_alignment
+    tuple val(meta), path("info.txt")                                     , emit: info_txt
+    tuple val(meta), path("snpAlignment.fasta.gz")                        , emit: snp_alignment
+    tuple val(meta), path("snpAlignmentIncludingRefGenome.fasta.gz")      , emit: snp_genome_alignment
+    tuple val(meta), path("snpStatistics.tsv")                            , emit: snpstatistics
+    tuple val(meta), path("snpTable.tsv")                                 , emit: snptable
+    tuple val(meta), path("snpTableForSnpEff.tsv")                        , emit: snptable_snpeff
+    tuple val(meta), path("snpTableWithUncertaintyCalls.tsv")             , emit: snptable_uncertainty
+    tuple val(meta), path("structureGenotypes.tsv")                       , emit: structure_genotypes
+    tuple val(meta), path("structureGenotypes_noMissingData-Columns.tsv") , emit: structure_genotypes_nomissing
+    tuple val(meta), path("MultiVCFAnalyzer.json")                        , emit: json
     path "versions.yml"                                  , emit: versions
 
     when:
diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index 68001973bd9..8328cccf892 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -15,7 +15,7 @@ process NARFMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path('*.log'), emit: log
+    tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/pangolin/run/main.nf b/modules/nf-core/pangolin/run/main.nf
index 75ab8e2a841..c7a1eb2992c 100644
--- a/modules/nf-core/pangolin/run/main.nf
+++ b/modules/nf-core/pangolin/run/main.nf
@@ -12,7 +12,7 @@ process PANGOLIN_RUN {
     path(db)
 
     output:
-    tuple val(meta), path('*.csv'), emit: report
+    tuple val(meta), path("*.csv"), emit: report
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf
index c8eddb1a12e..8034df59399 100644
--- a/modules/nf-core/picard/bedtointervallist/main.nf
+++ b/modules/nf-core/picard/bedtointervallist/main.nf
@@ -13,7 +13,7 @@ process PICARD_BEDTOINTERVALLIST {
     file  arguments_file
 
     output:
-    tuple val(meta), path('*.interval_list'), emit: interval_list
+    tuple val(meta), path("*.interval_list"), emit: interval_list
     path  "versions.yml"                    , emit: versions
 
     when:
diff --git a/modules/nf-core/platypus/main.nf b/modules/nf-core/platypus/main.nf
index 4813b466668..4efb250fc4c 100644
--- a/modules/nf-core/platypus/main.nf
+++ b/modules/nf-core/platypus/main.nf
@@ -20,9 +20,9 @@ process PLATYPUS {
     path skipregions_file
 
     output:
-    tuple val(meta), path('*.vcf.gz')            , emit: vcf
-    tuple val(meta), path('*.vcf.gz.tbi')        , emit: tbi
-    tuple val(meta), path('*.log')               , emit: log
+    tuple val(meta), path("*.vcf.gz")            , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi")        , emit: tbi
+    tuple val(meta), path("*.log")               , emit: log
     path  "versions.yml"                         , emit: version
 
     when:
diff --git a/modules/nf-core/popscle/demuxlet/main.nf b/modules/nf-core/popscle/demuxlet/main.nf
index a941ebb17bd..00da38c17a7 100644
--- a/modules/nf-core/popscle/demuxlet/main.nf
+++ b/modules/nf-core/popscle/demuxlet/main.nf
@@ -11,7 +11,7 @@ process POPSCLE_DEMUXLET {
     tuple val(meta), val(plp_prefix), path(bam), path(donor_genotype)
 
     output:
-    tuple val(meta), path('*.best'), emit: demuxlet_result
+    tuple val(meta), path("*.best"), emit: demuxlet_result
     path 'versions.yml'            , emit: versions
 
     when:
diff --git a/modules/nf-core/popscle/dscpileup/main.nf b/modules/nf-core/popscle/dscpileup/main.nf
index 2f7fbf3a7fe..1eb2f83f902 100644
--- a/modules/nf-core/popscle/dscpileup/main.nf
+++ b/modules/nf-core/popscle/dscpileup/main.nf
@@ -11,10 +11,10 @@ process POPSCLE_DSCPILEUP {
     tuple val(meta), path(bam), path(vcf)
 
     output:
-    tuple val(meta), path('*.cel.gz'), emit: cel
-    tuple val(meta), path('*.plp.gz'), emit: plp
-    tuple val(meta), path('*.var.gz'), emit: var
-    tuple val(meta), path('*.umi.gz'), emit: umi
+    tuple val(meta), path("*.cel.gz"), emit: cel
+    tuple val(meta), path("*.plp.gz"), emit: plp
+    tuple val(meta), path("*.var.gz"), emit: var
+    tuple val(meta), path("*.umi.gz"), emit: umi
     path 'versions.yml'              , emit: versions
 
     when:
diff --git a/modules/nf-core/popscle/freemuxlet/main.nf b/modules/nf-core/popscle/freemuxlet/main.nf
index d94d36a126f..69c0fbc5c16 100644
--- a/modules/nf-core/popscle/freemuxlet/main.nf
+++ b/modules/nf-core/popscle/freemuxlet/main.nf
@@ -11,11 +11,11 @@ process POPSCLE_FREEMUXLET {
     tuple val(meta), path(plp), val(n_sample)
 
     output:
-    tuple val(meta), path('*.clust1.samples.gz')  , emit: result
-    tuple val(meta), path('*.clust1.vcf.gz')      , emit: vcf
-    tuple val(meta), path('*.lmix')               , emit: lmix
-    tuple val(meta), path('*.clust0.samples.gz')  , emit: singlet_result   , optional: true
-    tuple val(meta), path('*.clust0.vcf.gz')      , emit: singlet_vcf      , optional: true
+    tuple val(meta), path("*.clust1.samples.gz")  , emit: result
+    tuple val(meta), path("*.clust1.vcf.gz")      , emit: vcf
+    tuple val(meta), path("*.lmix")               , emit: lmix
+    tuple val(meta), path("*.clust0.samples.gz")  , emit: singlet_result   , optional: true
+    tuple val(meta), path("*.clust0.vcf.gz")      , emit: singlet_vcf      , optional: true
     path 'versions.yml'                           , emit: versions
 
     when:
diff --git a/modules/nf-core/pretextsnapshot/main.nf b/modules/nf-core/pretextsnapshot/main.nf
index b8dbd1df55b..30ffae3aa6a 100644
--- a/modules/nf-core/pretextsnapshot/main.nf
+++ b/modules/nf-core/pretextsnapshot/main.nf
@@ -11,7 +11,7 @@ process PRETEXTSNAPSHOT {
     tuple val(meta), path(pretext_map)
 
     output:
-    tuple val(meta), path('*.{jpeg,png,bmp}'), emit: image
+    tuple val(meta), path("*.{jpeg,png,bmp}"), emit: image
     path "versions.yml" , emit: versions
 
     when:
diff --git a/modules/nf-core/pypgx/computecontrolstatistics/main.nf b/modules/nf-core/pypgx/computecontrolstatistics/main.nf
index 54397240b3d..2e6b8c4029d 100644
--- a/modules/nf-core/pypgx/computecontrolstatistics/main.nf
+++ b/modules/nf-core/pypgx/computecontrolstatistics/main.nf
@@ -13,7 +13,7 @@ process PYPGX_COMPUTECONTROLSTATISTICS {
     val(assembly_version)
 
     output:
-    tuple val(meta), path('*.zip'), emit: control_stats
+    tuple val(meta), path("*.zip"), emit: control_stats
     path("versions.yml"), emit: versions
 
     when:
diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/main.nf b/modules/nf-core/pypgx/preparedepthofcoverage/main.nf
index 1682eae234b..ba1825c3be7 100644
--- a/modules/nf-core/pypgx/preparedepthofcoverage/main.nf
+++ b/modules/nf-core/pypgx/preparedepthofcoverage/main.nf
@@ -13,7 +13,7 @@ process PYPGX_PREPAREDEPTHOFCOVERAGE {
     val(assembly_version)
 
     output:
-    tuple val(meta), path('*.zip'), emit: coverage
+    tuple val(meta), path("*.zip"), emit: coverage
     path("versions.yml"), emit: versions
 
     when:
diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf
index de29e355150..9e96be990ea 100644
--- a/modules/nf-core/racon/main.nf
+++ b/modules/nf-core/racon/main.nf
@@ -11,7 +11,7 @@ process RACON {
     tuple val(meta), path(reads), path(assembly), path(paf)
 
     output:
-    tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
+    tuple val(meta), path("*_assembly_consensus.fasta.gz") , emit: improved_assembly
     path "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf
index 9685b9b2264..f92fb6516d3 100644
--- a/modules/nf-core/rasusa/main.nf
+++ b/modules/nf-core/rasusa/main.nf
@@ -12,7 +12,7 @@ process RASUSA {
     val   depth_cutoff
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     path "versions.yml"                , emit: versions
 
     when:
diff --git a/modules/nf-core/ribotricer/detectorfs/main.nf b/modules/nf-core/ribotricer/detectorfs/main.nf
index d86a64e58fc..8a0e67d13df 100644
--- a/modules/nf-core/ribotricer/detectorfs/main.nf
+++ b/modules/nf-core/ribotricer/detectorfs/main.nf
@@ -12,16 +12,16 @@ process RIBOTRICER_DETECTORFS {
     tuple val(meta2), path(candidate_orfs)
 
     output:
-    tuple val(meta), path('*_protocol.txt')             , emit: protocol, optional: true
-    tuple val(meta), path('*_bam_summary.txt')          , emit: bam_summary
-    tuple val(meta), path('*_read_length_dist.pdf')     , emit: read_length_dist
-    tuple val(meta), path('*_metagene_profiles_5p.tsv') , emit: metagene_profile_5p
-    tuple val(meta), path('*_metagene_profiles_3p.tsv') , emit: metagene_profile_3p
-    tuple val(meta), path('*_metagene_plots.pdf')       , emit: metagene_plots
-    tuple val(meta), path('*_psite_offsets.txt')        , emit: psite_offsets, optional: true
-    tuple val(meta), path('*_pos.wig')                  , emit: pos_wig
-    tuple val(meta), path('*_neg.wig')                  , emit: neg_wig
-    tuple val(meta), path('*_translating_ORFs.tsv')     , emit: orfs
+    tuple val(meta), path("*_protocol.txt")             , emit: protocol, optional: true
+    tuple val(meta), path("*_bam_summary.txt")          , emit: bam_summary
+    tuple val(meta), path("*_read_length_dist.pdf")     , emit: read_length_dist
+    tuple val(meta), path("*_metagene_profiles_5p.tsv") , emit: metagene_profile_5p
+    tuple val(meta), path("*_metagene_profiles_3p.tsv") , emit: metagene_profile_3p
+    tuple val(meta), path("*_metagene_plots.pdf")       , emit: metagene_plots
+    tuple val(meta), path("*_psite_offsets.txt")        , emit: psite_offsets, optional: true
+    tuple val(meta), path("*_pos.wig")                  , emit: pos_wig
+    tuple val(meta), path("*_neg.wig")                  , emit: neg_wig
+    tuple val(meta), path("*_translating_ORFs.tsv")     , emit: orfs
     path "versions.yml"                                 , emit: versions
 
     when:
diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf
index 85bf6b507e6..5ca624e1fac 100644
--- a/modules/nf-core/sentieon/datametrics/main.nf
+++ b/modules/nf-core/sentieon/datametrics/main.nf
@@ -15,16 +15,16 @@ process SENTIEON_DATAMETRICS {
     val plot_results
 
     output:
-    tuple val(meta), path('*mq_metrics.txt') , emit: mq_metrics
-    tuple val(meta), path('*qd_metrics.txt') , emit: qd_metrics
-    tuple val(meta), path('*gc_summary.txt') , emit: gc_summary
-    tuple val(meta), path('*gc_metrics.txt') , emit: gc_metrics
-    tuple val(meta), path('*aln_metrics.txt'), emit: aln_metrics
-    tuple val(meta), path('*is_metrics.txt') , emit: is_metrics
-    tuple val(meta), path('*mq_metrics.pdf') , emit: mq_plot, optional: true
-    tuple val(meta), path('*qd_metrics.pdf') , emit: qd_plot, optional: true
-    tuple val(meta), path('*is_metrics.pdf') , emit: is_plot, optional: true
-    tuple val(meta), path('*gc_metrics.pdf') , emit: gc_plot, optional: true
+    tuple val(meta), path("*mq_metrics.txt") , emit: mq_metrics
+    tuple val(meta), path("*qd_metrics.txt") , emit: qd_metrics
+    tuple val(meta), path("*gc_summary.txt") , emit: gc_summary
+    tuple val(meta), path("*gc_metrics.txt") , emit: gc_metrics
+    tuple val(meta), path("*aln_metrics.txt"), emit: aln_metrics
+    tuple val(meta), path("*is_metrics.txt") , emit: is_metrics
+    tuple val(meta), path("*mq_metrics.pdf") , emit: mq_plot, optional: true
+    tuple val(meta), path("*qd_metrics.pdf") , emit: qd_plot, optional: true
+    tuple val(meta), path("*is_metrics.pdf") , emit: is_plot, optional: true
+    tuple val(meta), path("*gc_metrics.pdf") , emit: gc_plot, optional: true
     path  "versions.yml"                     , emit: versions
 
     when:
diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf
index 9f268f5a858..cba7b5fefc2 100644
--- a/modules/nf-core/sentieon/wgsmetrics/main.nf
+++ b/modules/nf-core/sentieon/wgsmetrics/main.nf
@@ -15,7 +15,7 @@ process SENTIEON_WGSMETRICS {
     tuple val(meta4), path(intervals_list)
 
     output:
-    tuple val(meta), path('*.txt'), emit: wgs_metrics
+    tuple val(meta), path("*.txt"), emit: wgs_metrics
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/sgdemux/main.nf b/modules/nf-core/sgdemux/main.nf
index e817e7bd454..b987d623036 100644
--- a/modules/nf-core/sgdemux/main.nf
+++ b/modules/nf-core/sgdemux/main.nf
@@ -12,12 +12,12 @@ process SGDEMUX {
     tuple val(meta), path(sample_sheet), path(fastqs_dir)
 
     output:
-    tuple val(meta), path('output/*_R*.fastq.gz')                   , emit: sample_fastq
-    tuple val(meta), path('output/metrics.tsv')                     , emit: metrics
-    tuple val(meta), path('output/most_frequent_unmatched.tsv')     , emit: most_frequent_unmatched
-    tuple val(meta), path('output/per_project_metrics.tsv')         , emit: per_project_metrics
-    tuple val(meta), path('output/per_sample_metrics.tsv')          , emit: per_sample_metrics
-    tuple val(meta), path('output/sample_barcode_hop_metrics.tsv')  , emit: sample_barcode_hop_metrics
+    tuple val(meta), path("output/*_R*.fastq.gz")                   , emit: sample_fastq
+    tuple val(meta), path("output/metrics.tsv")                     , emit: metrics
+    tuple val(meta), path("output/most_frequent_unmatched.tsv")     , emit: most_frequent_unmatched
+    tuple val(meta), path("output/per_project_metrics.tsv")         , emit: per_project_metrics
+    tuple val(meta), path("output/per_sample_metrics.tsv")          , emit: per_sample_metrics
+    tuple val(meta), path("output/sample_barcode_hop_metrics.tsv")  , emit: sample_barcode_hop_metrics
     path "versions.yml"                                             , emit: versions
 
     when:
diff --git a/modules/nf-core/snpeff/download/main.nf b/modules/nf-core/snpeff/download/main.nf
index e42259337dc..eef7711a54b 100644
--- a/modules/nf-core/snpeff/download/main.nf
+++ b/modules/nf-core/snpeff/download/main.nf
@@ -11,7 +11,7 @@ process SNPEFF_DOWNLOAD {
     tuple val(meta), val(snpeff_db)
 
     output:
-    tuple val(meta), path('snpeff_cache'), emit: cache
+    tuple val(meta), path("snpeff_cache"), emit: cache
     path "versions.yml"                  , emit: versions
 
     when:
diff --git a/modules/nf-core/sourmash/gather/main.nf b/modules/nf-core/sourmash/gather/main.nf
index 7dd13c27cfd..c40e8685e97 100644
--- a/modules/nf-core/sourmash/gather/main.nf
+++ b/modules/nf-core/sourmash/gather/main.nf
@@ -16,11 +16,11 @@ process SOURMASH_GATHER {
     val save_prefetch_csv
 
     output:
-    tuple val(meta), path('*.csv.gz')             , optional:true, emit: result
-    tuple val(meta), path('*_unassigned.sig.zip') , optional:true, emit: unassigned
-    tuple val(meta), path('*_matches.sig.zip')    , optional:true, emit: matches
-    tuple val(meta), path('*_prefetch.sig.zip')   , optional:true, emit: prefetch
-    tuple val(meta), path('*_prefetch.csv.gz')    , optional:true, emit: prefetchcsv
+    tuple val(meta), path("*.csv.gz")             , optional:true, emit: result
+    tuple val(meta), path("*_unassigned.sig.zip") , optional:true, emit: unassigned
+    tuple val(meta), path("*_matches.sig.zip")    , optional:true, emit: matches
+    tuple val(meta), path("*_prefetch.sig.zip")   , optional:true, emit: prefetch
+    tuple val(meta), path("*_prefetch.csv.gz")    , optional:true, emit: prefetchcsv
     path "versions.yml"                           , emit: versions
 
     when:
diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf
index 36cdfe444cc..1199f91774b 100644
--- a/modules/nf-core/spades/main.nf
+++ b/modules/nf-core/spades/main.nf
@@ -13,13 +13,13 @@ process SPADES {
     path hmm
 
     output:
-    tuple val(meta), path('*.scaffolds.fa.gz')    , optional:true, emit: scaffolds
-    tuple val(meta), path('*.contigs.fa.gz')      , optional:true, emit: contigs
-    tuple val(meta), path('*.transcripts.fa.gz')  , optional:true, emit: transcripts
-    tuple val(meta), path('*.gene_clusters.fa.gz'), optional:true, emit: gene_clusters
-    tuple val(meta), path('*.assembly.gfa.gz')    , optional:true, emit: gfa
-    tuple val(meta), path('*.warnings.log')         , optional:true, emit: warnings
-    tuple val(meta), path('*.spades.log')         , emit: log
+    tuple val(meta), path("*.scaffolds.fa.gz")    , optional:true, emit: scaffolds
+    tuple val(meta), path("*.contigs.fa.gz")      , optional:true, emit: contigs
+    tuple val(meta), path("*.transcripts.fa.gz")  , optional:true, emit: transcripts
+    tuple val(meta), path("*.gene_clusters.fa.gz"), optional:true, emit: gene_clusters
+    tuple val(meta), path("*.assembly.gfa.gz")    , optional:true, emit: gfa
+    tuple val(meta), path("*.warnings.log")         , optional:true, emit: warnings
+    tuple val(meta), path("*.spades.log")         , emit: log
     path  "versions.yml"                          , emit: versions
 
     when:
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index d5b65bab270..d6782635c79 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -13,7 +13,7 @@ process SRATOOLS_FASTERQDUMP {
     path certificate
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     path "versions.yml"                , emit: versions
 
     when:
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index 417071ba96f..e4287a9d522 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -16,24 +16,24 @@ process STAR_ALIGN {
     val seq_center
 
     output:
-    tuple val(meta), path('*Log.final.out')   , emit: log_final
-    tuple val(meta), path('*Log.out')         , emit: log_out
-    tuple val(meta), path('*Log.progress.out'), emit: log_progress
+    tuple val(meta), path("*Log.final.out")   , emit: log_final
+    tuple val(meta), path("*Log.out")         , emit: log_out
+    tuple val(meta), path("*Log.progress.out"), emit: log_progress
     path  "versions.yml"                      , emit: versions
 
-    tuple val(meta), path('*d.out.bam')                              , optional:true, emit: bam
+    tuple val(meta), path("*d.out.bam")                              , optional:true, emit: bam
     tuple val(meta), path("${prefix}.sortedByCoord.out.bam")         , optional:true, emit: bam_sorted
     tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned
-    tuple val(meta), path('*toTranscriptome.out.bam')                , optional:true, emit: bam_transcript
-    tuple val(meta), path('*Aligned.unsort.out.bam')                 , optional:true, emit: bam_unsorted
-    tuple val(meta), path('*fastq.gz')                               , optional:true, emit: fastq
-    tuple val(meta), path('*.tab')                                   , optional:true, emit: tab
-    tuple val(meta), path('*.SJ.out.tab')                            , optional:true, emit: spl_junc_tab
-    tuple val(meta), path('*.ReadsPerGene.out.tab')                  , optional:true, emit: read_per_gene_tab
-    tuple val(meta), path('*.out.junction')                          , optional:true, emit: junction
-    tuple val(meta), path('*.out.sam')                               , optional:true, emit: sam
-    tuple val(meta), path('*.wig')                                   , optional:true, emit: wig
-    tuple val(meta), path('*.bg')                                    , optional:true, emit: bedgraph
+    tuple val(meta), path("*toTranscriptome.out.bam")                , optional:true, emit: bam_transcript
+    tuple val(meta), path("*Aligned.unsort.out.bam")                 , optional:true, emit: bam_unsorted
+    tuple val(meta), path("*fastq.gz")                               , optional:true, emit: fastq
+    tuple val(meta), path("*.tab")                                   , optional:true, emit: tab
+    tuple val(meta), path("*.SJ.out.tab")                            , optional:true, emit: spl_junc_tab
+    tuple val(meta), path("*.ReadsPerGene.out.tab")                  , optional:true, emit: read_per_gene_tab
+    tuple val(meta), path("*.out.junction")                          , optional:true, emit: junction
+    tuple val(meta), path("*.out.sam")                               , optional:true, emit: sam
+    tuple val(meta), path("*.wig")                                   , optional:true, emit: wig
+    tuple val(meta), path("*.bg")                                    , optional:true, emit: bedgraph
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/star/starsolo/main.nf b/modules/nf-core/star/starsolo/main.nf
index 94a9e2d0859..0f6994e9e94 100644
--- a/modules/nf-core/star/starsolo/main.nf
+++ b/modules/nf-core/star/starsolo/main.nf
@@ -13,11 +13,11 @@ process STARSOLO {
     tuple val(meta2), path(index)
 
     output:
-    tuple val(meta),  path('*.Solo.out')         , emit: counts
-    tuple val(meta),  path('*Log.final.out')     , emit: log_final
-    tuple val(meta),  path('*Log.out')           , emit: log_out
-    tuple val(meta),  path('*Log.progress.out')  , emit: log_progress
-    tuple val(meta),  path('*/Gene/Summary.csv') , emit: summary
+    tuple val(meta),  path("*.Solo.out")         , emit: counts
+    tuple val(meta),  path("*Log.final.out")     , emit: log_final
+    tuple val(meta),  path("*Log.out")           , emit: log_out
+    tuple val(meta),  path("*Log.progress.out")  , emit: log_progress
+    tuple val(meta),  path("*/Gene/Summary.csv") , emit: summary
     path "versions.yml"                          , emit: versions
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/sylph/sketch/main.nf b/modules/nf-core/sylph/sketch/main.nf
index 6d8a831c791..602a0424963 100644
--- a/modules/nf-core/sylph/sketch/main.nf
+++ b/modules/nf-core/sylph/sketch/main.nf
@@ -12,7 +12,7 @@ process SYLPH_SKETCH {
     path(reference)
 
     output:
-    tuple val(meta), path('my_sketches/*.sylsp'), path('database.syldb'), emit: sketch_fastq_genome
+    tuple val(meta), path("my_sketches/*.sylsp"), path("database.syldb"), emit: sketch_fastq_genome
     path "versions.yml"                                                 , emit: versions
 
     when:
diff --git a/modules/nf-core/umitools/prepareforrsem/main.nf b/modules/nf-core/umitools/prepareforrsem/main.nf
index 07c4381ad9b..dde6187e598 100644
--- a/modules/nf-core/umitools/prepareforrsem/main.nf
+++ b/modules/nf-core/umitools/prepareforrsem/main.nf
@@ -11,8 +11,8 @@ process UMITOOLS_PREPAREFORRSEM {
     tuple val(meta), path(bam), path(bai)
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
-    tuple val(meta), path('*.log'), emit: log
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: log
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf
index f8971804b2a..0342919488e 100644
--- a/modules/nf-core/unicycler/main.nf
+++ b/modules/nf-core/unicycler/main.nf
@@ -11,9 +11,9 @@ process UNICYCLER {
     tuple val(meta), path(shortreads), path(longreads)
 
     output:
-    tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds
-    tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa
-    tuple val(meta), path('*.log')            , emit: log
+    tuple val(meta), path("*.scaffolds.fa.gz"), emit: scaffolds
+    tuple val(meta), path("*.assembly.gfa.gz"), emit: gfa
+    tuple val(meta), path("*.log")            , emit: log
     path  "versions.yml"                      , emit: versions
 
     when:
diff --git a/modules/nf-core/vireo/main.nf b/modules/nf-core/vireo/main.nf
index 2319a5f554a..3a98976a29d 100644
--- a/modules/nf-core/vireo/main.nf
+++ b/modules/nf-core/vireo/main.nf
@@ -10,10 +10,10 @@ process VIREO {
     input:
     tuple val(meta), path(cell_data), val(n_donor), path(donor_file), path(vartrix_data)
     output:
-    tuple val(meta), path('*_summary.tsv')        , emit: summary
-    tuple val(meta), path('*_donor_ids.tsv')      , emit: donor_ids
-    tuple val(meta), path('*_prob_singlet.tsv.gz'), emit: prob_singlets
-    tuple val(meta), path('*_prob_doublet.tsv.gz'), emit: prob_doublets
+    tuple val(meta), path("*_summary.tsv")        , emit: summary
+    tuple val(meta), path("*_donor_ids.tsv")      , emit: donor_ids
+    tuple val(meta), path("*_prob_singlet.tsv.gz"), emit: prob_singlets
+    tuple val(meta), path("*_prob_doublet.tsv.gz"), emit: prob_doublets
     path 'versions.yml'                           , emit: versions
 
     when:
diff --git a/modules/nf-core/vsearch/cluster/main.nf b/modules/nf-core/vsearch/cluster/main.nf
index 23b838c660e..0c271272eff 100644
--- a/modules/nf-core/vsearch/cluster/main.nf
+++ b/modules/nf-core/vsearch/cluster/main.nf
@@ -11,18 +11,18 @@ process VSEARCH_CLUSTER {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('*.aln.gz')                , optional: true, emit: aln
-    tuple val(meta), path('*.biom.gz')               , optional: true, emit: biom
-    tuple val(meta), path('*.mothur.tsv.gz')         , optional: true, emit: mothur
-    tuple val(meta), path('*.otu.tsv.gz')            , optional: true, emit: otu
-    tuple val(meta), path('*.bam')                   , optional: true, emit: bam
-    tuple val(meta), path('*.out.tsv.gz')            , optional: true, emit: out
-    tuple val(meta), path('*.blast.tsv.gz')          , optional: true, emit: blast
-    tuple val(meta), path('*.uc.tsv.gz')             , optional: true, emit: uc
-    tuple val(meta), path('*.centroids.fasta.gz')    , optional: true, emit: centroids
-    tuple val(meta), path('*.clusters.fasta*.gz')    , optional: true, emit: clusters
-    tuple val(meta), path('*.profile.txt.gz')        , optional: true, emit: profile
-    tuple val(meta), path('*.msa.fasta.gz')          , optional: true, emit: msa
+    tuple val(meta), path("*.aln.gz")                , optional: true, emit: aln
+    tuple val(meta), path("*.biom.gz")               , optional: true, emit: biom
+    tuple val(meta), path("*.mothur.tsv.gz")         , optional: true, emit: mothur
+    tuple val(meta), path("*.otu.tsv.gz")            , optional: true, emit: otu
+    tuple val(meta), path("*.bam")                   , optional: true, emit: bam
+    tuple val(meta), path("*.out.tsv.gz")            , optional: true, emit: out
+    tuple val(meta), path("*.blast.tsv.gz")          , optional: true, emit: blast
+    tuple val(meta), path("*.uc.tsv.gz")             , optional: true, emit: uc
+    tuple val(meta), path("*.centroids.fasta.gz")    , optional: true, emit: centroids
+    tuple val(meta), path("*.clusters.fasta*.gz")    , optional: true, emit: clusters
+    tuple val(meta), path("*.profile.txt.gz")        , optional: true, emit: profile
+    tuple val(meta), path("*.msa.fasta.gz")          , optional: true, emit: msa
     path "versions.yml"                              , emit: versions
 
     when:
diff --git a/modules/nf-core/vsearch/dereplicate/main.nf b/modules/nf-core/vsearch/dereplicate/main.nf
index 468c7a2fe46..7b6c2d30122 100644
--- a/modules/nf-core/vsearch/dereplicate/main.nf
+++ b/modules/nf-core/vsearch/dereplicate/main.nf
@@ -11,8 +11,8 @@ process VSEARCH_DEREPLICATE {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('*.derep.fasta')   , emit: fasta
-    tuple val(meta), path('*.derep.uc')      , emit: clustering
+    tuple val(meta), path("*.derep.fasta")   , emit: fasta
+    tuple val(meta), path("*.derep.uc")      , emit: clustering
     path "*.derep.log"                       , emit: log
     path "versions.yml"                      , emit: versions
 
diff --git a/modules/nf-core/vsearch/fastqfilter/main.nf b/modules/nf-core/vsearch/fastqfilter/main.nf
index 7f1103a4b93..5aacbcbfadb 100644
--- a/modules/nf-core/vsearch/fastqfilter/main.nf
+++ b/modules/nf-core/vsearch/fastqfilter/main.nf
@@ -12,7 +12,7 @@ process VSEARCH_FASTQFILTER {
     tuple val(meta), path(fastq)
 
     output:
-    tuple val(meta), path('*.fasta')   , emit: fasta
+    tuple val(meta), path("*.fasta")   , emit: fasta
     path "*.log"                       , emit: log
     path "versions.yml"                , emit: versions
 
diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf
index 9e6147d1194..fa0c813f94c 100644
--- a/modules/nf-core/vsearch/sintax/main.nf
+++ b/modules/nf-core/vsearch/sintax/main.nf
@@ -12,7 +12,7 @@ process VSEARCH_SINTAX {
     path db
 
     output:
-    tuple val(meta), path('*.tsv')   , optional: true, emit: tsv
+    tuple val(meta), path("*.tsv")   , optional: true, emit: tsv
     path "versions.yml"              , emit: versions
 
     when:
diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf
index 549d9756cbf..28260e15055 100644
--- a/modules/nf-core/vsearch/usearchglobal/main.nf
+++ b/modules/nf-core/vsearch/usearchglobal/main.nf
@@ -15,15 +15,15 @@ process VSEARCH_USEARCHGLOBAL {
     val user_columns
 
     output:
-    tuple val(meta), path('*.aln')    , optional: true, emit: aln
-    tuple val(meta), path('*.biom')   , optional: true, emit: biom
-    tuple val(meta), path('*.lca')    , optional: true, emit: lca
-    tuple val(meta), path('*.mothur') , optional: true, emit: mothur
-    tuple val(meta), path('*.otu')    , optional: true, emit: otu
-    tuple val(meta), path('*.sam')    , optional: true, emit: sam
-    tuple val(meta), path('*.tsv')    , optional: true, emit: tsv
-    tuple val(meta), path('*.txt')    , optional: true, emit: txt
-    tuple val(meta), path('*.uc')     , optional: true, emit: uc
+    tuple val(meta), path("*.aln")    , optional: true, emit: aln
+    tuple val(meta), path("*.biom")   , optional: true, emit: biom
+    tuple val(meta), path("*.lca")    , optional: true, emit: lca
+    tuple val(meta), path("*.mothur") , optional: true, emit: mothur
+    tuple val(meta), path("*.otu")    , optional: true, emit: otu
+    tuple val(meta), path("*.sam")    , optional: true, emit: sam
+    tuple val(meta), path("*.tsv")    , optional: true, emit: tsv
+    tuple val(meta), path("*.txt")    , optional: true, emit: txt
+    tuple val(meta), path("*.uc")     , optional: true, emit: uc
     path "versions.yml"                               , emit: versions
 
     when:
diff --git a/tests/modules/nf-core/artic/guppyplex/main.nf b/tests/modules/nf-core/artic/guppyplex/main.nf
index bd60545d1d4..539c64538cc 100644
--- a/tests/modules/nf-core/artic/guppyplex/main.nf
+++ b/tests/modules/nf-core/artic/guppyplex/main.nf
@@ -9,7 +9,7 @@ process STAGE_FASTQ_DIR {
     tuple val(meta), path(fastq_file)
 
     output:
-    tuple val(meta), path('fastq'), emit: fastq_dir
+    tuple val(meta), path("fastq"), emit: fastq_dir
 
     script:
     """