READY FOR REVIEW: Adapt output declarations

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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
 

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:

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:

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:

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:

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:

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
 
 

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: