diff --git a/.nf-core.yml b/.nf-core.yml
index 7eb1f1078..a794b875c 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -5,11 +5,11 @@ lint:
     - lib/NfcoreTemplate.groovy
 update:
   nf-core/modules:
-    rseqc/bamstat: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/inferexperiment: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/innerdistance: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionannotation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionsaturation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readdistribution: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readduplication: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/tin: "ce8c781bb494c2cc1f0a951c31c7b2f4af12e8af"
+    rseqc/bamstat: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/inferexperiment: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/innerdistance: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/junctionannotation: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/junctionsaturation: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/readdistribution: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/readduplication: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/tin: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
diff --git a/modules.json b/modules.json
index 932aa105c..837b8daa7 100644
--- a/modules.json
+++ b/modules.json
@@ -4,118 +4,118 @@
     "repos": {
         "nf-core/modules": {
             "bbmap/bbsplit": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "cat/fastq": {
-                "git_sha": "826a5603db5cf5b4f1e55cef9cc0b7c37d3c7e70"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "gffread": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "gunzip": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/align": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/build": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/extractsplicesites": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "picard/markduplicates": {
-                "git_sha": "0d1e21686a586447b7592e40da9b3a7cdeedf03c"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "preseq/lcextrap": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "qualimap/rnaseq": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rsem/calculateexpression": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rsem/preparereference": {
-                "git_sha": "47a9cf8ecbe4de4dcb8b9cc6731fece82b934ab7"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/bamstat": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/inferexperiment": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/innerdistance": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/junctionannotation": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/junctionsaturation": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/readdistribution": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/readduplication": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/tin": {
-                "git_sha": "ce8c781bb494c2cc1f0a951c31c7b2f4af12e8af"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "salmon/index": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "salmon/quant": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/flagstat": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/idxstats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/index": {
-                "git_sha": "0fafaeebf52cc5ab554b83297ed02a48d852a848"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/sort": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/stats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "sortmerna": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "stringtie/stringtie": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "subread/featurecounts": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "trimgalore": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "ucsc/bedclip": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "ucsc/bedgraphtobigwig": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "umitools/dedup": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "umitools/extract": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "untar": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             }
         }
     }
diff --git a/modules/nf-core/modules/bbmap/bbsplit/main.nf b/modules/nf-core/modules/bbmap/bbsplit/main.nf
index 0c916dfe8..b55929ce9 100644
--- a/modules/nf-core/modules/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/modules/bbmap/bbsplit/main.nf
@@ -20,6 +20,9 @@ process BBMAP_BBSPLIT {
     tuple val(meta), path('*txt')             , optional:true, emit: stats
     path "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf
index d02598e1f..bf0877c3e 100644
--- a/modules/nf-core/modules/cat/fastq/main.nf
+++ b/modules/nf-core/modules/cat/fastq/main.nf
@@ -14,6 +14,9 @@ process CAT_FASTQ {
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
     path "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
index 934bb4672..327d51005 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     path "software_versions_mqc.yml", emit: mqc_yml
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     template 'dumpsoftwareversions.py'
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
index d250eca07..ed6b8c50b 100644
--- a/modules/nf-core/modules/fastqc/main.nf
+++ b/modules/nf-core/modules/fastqc/main.nf
@@ -15,6 +15,9 @@ process FASTQC {
     tuple val(meta), path("*.zip") , emit: zip
     path  "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     // Add soft-links to original FastQs for consistent naming in pipeline
diff --git a/modules/nf-core/modules/gffread/main.nf b/modules/nf-core/modules/gffread/main.nf
index e7893f8ba..7c575c97f 100644
--- a/modules/nf-core/modules/gffread/main.nf
+++ b/modules/nf-core/modules/gffread/main.nf
@@ -14,6 +14,9 @@ process GFFREAD {
     path "*.gtf"        , emit: gtf
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${gff.baseName}"
diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf
index 77a4e546b..9d4b06669 100644
--- a/modules/nf-core/modules/gunzip/main.nf
+++ b/modules/nf-core/modules/gunzip/main.nf
@@ -14,6 +14,9 @@ process GUNZIP {
     tuple val(meta), path("$gunzip"), emit: gunzip
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     gunzip = archive.toString() - '.gz'
diff --git a/modules/nf-core/modules/hisat2/align/main.nf b/modules/nf-core/modules/hisat2/align/main.nf
index ae8886169..7f6800189 100644
--- a/modules/nf-core/modules/hisat2/align/main.nf
+++ b/modules/nf-core/modules/hisat2/align/main.nf
@@ -20,6 +20,9 @@ process HISAT2_ALIGN {
     tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
     path  "versions.yml"                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/hisat2/build/main.nf b/modules/nf-core/modules/hisat2/build/main.nf
index 4e8cd02bb..50f65e3a1 100644
--- a/modules/nf-core/modules/hisat2/build/main.nf
+++ b/modules/nf-core/modules/hisat2/build/main.nf
@@ -19,6 +19,9 @@ process HISAT2_BUILD {
     path "hisat2"       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 0
diff --git a/modules/nf-core/modules/hisat2/extractsplicesites/main.nf b/modules/nf-core/modules/hisat2/extractsplicesites/main.nf
index 302c35f1f..941359779 100644
--- a/modules/nf-core/modules/hisat2/extractsplicesites/main.nf
+++ b/modules/nf-core/modules/hisat2/extractsplicesites/main.nf
@@ -16,6 +16,9 @@ process HISAT2_EXTRACTSPLICESITES {
     path "*.splice_sites.txt", emit: txt
     path "versions.yml"      , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/modules/picard/markduplicates/main.nf
index 3087bff4a..5196b6edf 100644
--- a/modules/nf-core/modules/picard/markduplicates/main.nf
+++ b/modules/nf-core/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -16,6 +16,9 @@ process PICARD_MARKDUPLICATES {
     tuple val(meta), path("*.metrics.txt"), emit: metrics
     path  "versions.yml"                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/preseq/lcextrap/main.nf b/modules/nf-core/modules/preseq/lcextrap/main.nf
index b5bd06206..d6dd19e23 100644
--- a/modules/nf-core/modules/preseq/lcextrap/main.nf
+++ b/modules/nf-core/modules/preseq/lcextrap/main.nf
@@ -16,6 +16,9 @@ process PRESEQ_LCEXTRAP {
     tuple val(meta), path("*.log")       , emit: log
     path  "versions.yml"                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/qualimap/rnaseq/main.nf b/modules/nf-core/modules/qualimap/rnaseq/main.nf
index d83fcd999..3b2f88ade 100644
--- a/modules/nf-core/modules/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/modules/qualimap/rnaseq/main.nf
@@ -15,6 +15,9 @@ process QUALIMAP_RNASEQ {
     tuple val(meta), path("${prefix}"), emit: results
     path  "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rsem/calculateexpression/main.nf b/modules/nf-core/modules/rsem/calculateexpression/main.nf
index 4b2ada47a..cf147a633 100644
--- a/modules/nf-core/modules/rsem/calculateexpression/main.nf
+++ b/modules/nf-core/modules/rsem/calculateexpression/main.nf
@@ -22,6 +22,9 @@ process RSEM_CALCULATEEXPRESSION {
     tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
     tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rsem/preparereference/main.nf b/modules/nf-core/modules/rsem/preparereference/main.nf
index a5b8922a0..2d2ca2056 100644
--- a/modules/nf-core/modules/rsem/preparereference/main.nf
+++ b/modules/nf-core/modules/rsem/preparereference/main.nf
@@ -16,6 +16,9 @@ process RSEM_PREPAREREFERENCE {
     path "*transcripts.fa", emit: transcript_fasta
     path "versions.yml"   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/nf-core/modules/rseqc/bamstat/main.nf b/modules/nf-core/modules/rseqc/bamstat/main.nf
index 1141a13f2..958221fde 100644
--- a/modules/nf-core/modules/rseqc/bamstat/main.nf
+++ b/modules/nf-core/modules/rseqc/bamstat/main.nf
@@ -14,6 +14,9 @@ process RSEQC_BAMSTAT {
     tuple val(meta), path("*.bam_stat.txt"), emit: txt
     path  "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/inferexperiment/main.nf b/modules/nf-core/modules/rseqc/inferexperiment/main.nf
index 2243c43e1..23c1b6882 100644
--- a/modules/nf-core/modules/rseqc/inferexperiment/main.nf
+++ b/modules/nf-core/modules/rseqc/inferexperiment/main.nf
@@ -15,6 +15,9 @@ process RSEQC_INFEREXPERIMENT {
     tuple val(meta), path("*.infer_experiment.txt"), emit: txt
     path  "versions.yml"                           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/innerdistance/main.nf b/modules/nf-core/modules/rseqc/innerdistance/main.nf
index 425737d68..b05661de1 100644
--- a/modules/nf-core/modules/rseqc/innerdistance/main.nf
+++ b/modules/nf-core/modules/rseqc/innerdistance/main.nf
@@ -19,6 +19,9 @@ process RSEQC_INNERDISTANCE {
     tuple val(meta), path("*.r")          , optional:true, emit: rscript
     path  "versions.yml"                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/junctionannotation/main.nf b/modules/nf-core/modules/rseqc/junctionannotation/main.nf
index d2562e5cb..c3401dc51 100644
--- a/modules/nf-core/modules/rseqc/junctionannotation/main.nf
+++ b/modules/nf-core/modules/rseqc/junctionannotation/main.nf
@@ -21,6 +21,9 @@ process RSEQC_JUNCTIONANNOTATION {
     tuple val(meta), path("*events.pdf")   , optional:true, emit: events_pdf
     path  "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/junctionsaturation/main.nf b/modules/nf-core/modules/rseqc/junctionsaturation/main.nf
index 695762b5c..11b629040 100644
--- a/modules/nf-core/modules/rseqc/junctionsaturation/main.nf
+++ b/modules/nf-core/modules/rseqc/junctionsaturation/main.nf
@@ -16,6 +16,9 @@ process RSEQC_JUNCTIONSATURATION {
     tuple val(meta), path("*.r")  , emit: rscript
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/readdistribution/main.nf b/modules/nf-core/modules/rseqc/readdistribution/main.nf
index 333193e30..3198c5c66 100644
--- a/modules/nf-core/modules/rseqc/readdistribution/main.nf
+++ b/modules/nf-core/modules/rseqc/readdistribution/main.nf
@@ -15,6 +15,9 @@ process RSEQC_READDISTRIBUTION {
     tuple val(meta), path("*.read_distribution.txt"), emit: txt
     path  "versions.yml"                            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/readduplication/main.nf b/modules/nf-core/modules/rseqc/readduplication/main.nf
index 134f2e8db..cb989a5f2 100644
--- a/modules/nf-core/modules/rseqc/readduplication/main.nf
+++ b/modules/nf-core/modules/rseqc/readduplication/main.nf
@@ -17,6 +17,9 @@ process RSEQC_READDUPLICATION {
     tuple val(meta), path("*.r")             , emit: rscript
     path  "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/rseqc/tin/main.nf b/modules/nf-core/modules/rseqc/tin/main.nf
index b7bff0f31..da58fc06b 100644
--- a/modules/nf-core/modules/rseqc/tin/main.nf
+++ b/modules/nf-core/modules/rseqc/tin/main.nf
@@ -16,6 +16,9 @@ process RSEQC_TIN {
     tuple val(meta), path("*.xls"), emit: xls
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/salmon/index/main.nf b/modules/nf-core/modules/salmon/index/main.nf
index b0a2f973c..737087f96 100644
--- a/modules/nf-core/modules/salmon/index/main.nf
+++ b/modules/nf-core/modules/salmon/index/main.nf
@@ -15,6 +15,9 @@ process SALMON_INDEX {
     path "salmon"       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
diff --git a/modules/nf-core/modules/salmon/quant/main.nf b/modules/nf-core/modules/salmon/quant/main.nf
index 6cae4f72d..bd4792c52 100644
--- a/modules/nf-core/modules/salmon/quant/main.nf
+++ b/modules/nf-core/modules/salmon/quant/main.nf
@@ -19,6 +19,9 @@ process SALMON_QUANT {
     tuple val(meta), path("${prefix}"), emit: results
     path  "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/samtools/flagstat/main.nf b/modules/nf-core/modules/samtools/flagstat/main.nf
index 03721d0b2..c267922b3 100644
--- a/modules/nf-core/modules/samtools/flagstat/main.nf
+++ b/modules/nf-core/modules/samtools/flagstat/main.nf
@@ -14,10 +14,18 @@ process SAMTOOLS_FLAGSTAT {
     tuple val(meta), path("*.flagstat"), emit: flagstat
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
-    samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
+    samtools \\
+        flagstat \\
+        --threads ${task.cpus-1} \\
+        $bam \\
+        > ${bam}.flagstat
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/nf-core/modules/samtools/idxstats/main.nf b/modules/nf-core/modules/samtools/idxstats/main.nf
index cd0686791..8a057413e 100644
--- a/modules/nf-core/modules/samtools/idxstats/main.nf
+++ b/modules/nf-core/modules/samtools/idxstats/main.nf
@@ -14,10 +14,17 @@ process SAMTOOLS_IDXSTATS {
     tuple val(meta), path("*.idxstats"), emit: idxstats
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
-    samtools idxstats $bam > ${bam}.idxstats
+    samtools \\
+        idxstats \\
+        $bam \\
+        > ${bam}.idxstats
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/nf-core/modules/samtools/index/main.nf b/modules/nf-core/modules/samtools/index/main.nf
index db025a8f9..dfe0234f7 100644
--- a/modules/nf-core/modules/samtools/index/main.nf
+++ b/modules/nf-core/modules/samtools/index/main.nf
@@ -16,10 +16,17 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path("*.crai"), optional:true, emit: crai
     path  "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
-    samtools index -@ ${task.cpus-1} $args $input
+    samtools \\
+        index \\
+        -@ ${task.cpus-1} \\
+        $args \\
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/samtools/sort/main.nf b/modules/nf-core/modules/samtools/sort/main.nf
index 0c2cf25e3..0f2237cc1 100644
--- a/modules/nf-core/modules/samtools/sort/main.nf
+++ b/modules/nf-core/modules/samtools/sort/main.nf
@@ -14,9 +14,13 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/modules/samtools/stats/main.nf
index 83c870025..f6fe3bfef 100644
--- a/modules/nf-core/modules/samtools/stats/main.nf
+++ b/modules/nf-core/modules/samtools/stats/main.nf
@@ -15,11 +15,19 @@ process SAMTOOLS_STATS {
     tuple val(meta), path("*.stats"), emit: stats
     path  "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def reference = fasta ? "--reference ${fasta}" : ""
     """
-    samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats
+    samtools \\
+        stats \\
+        --threads ${task.cpus-1} \\
+        ${reference} \\
+        ${input} \\
+        > ${input}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/sortmerna/main.nf b/modules/nf-core/modules/sortmerna/main.nf
index 5c0950d87..419d29149 100644
--- a/modules/nf-core/modules/sortmerna/main.nf
+++ b/modules/nf-core/modules/sortmerna/main.nf
@@ -16,6 +16,9 @@ process SORTMERNA {
     tuple val(meta), path("*.log")     , emit: log
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/stringtie/stringtie/main.nf b/modules/nf-core/modules/stringtie/stringtie/main.nf
index 9d62a966a..f37e347a5 100644
--- a/modules/nf-core/modules/stringtie/stringtie/main.nf
+++ b/modules/nf-core/modules/stringtie/stringtie/main.nf
@@ -18,6 +18,9 @@ process STRINGTIE {
     tuple val(meta), path("*.ballgown")       , emit: ballgown
     path  "versions.yml"                      , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/subread/featurecounts/main.nf b/modules/nf-core/modules/subread/featurecounts/main.nf
index 53eb279e1..18e2a92bb 100644
--- a/modules/nf-core/modules/subread/featurecounts/main.nf
+++ b/modules/nf-core/modules/subread/featurecounts/main.nf
@@ -15,6 +15,9 @@ process SUBREAD_FEATURECOUNTS {
     tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
     path "versions.yml"                                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/trimgalore/main.nf b/modules/nf-core/modules/trimgalore/main.nf
index ee40b780b..9487c7990 100644
--- a/modules/nf-core/modules/trimgalore/main.nf
+++ b/modules/nf-core/modules/trimgalore/main.nf
@@ -18,6 +18,9 @@ process TRIMGALORE {
     tuple val(meta), path("*.html"), emit: html optional true
     tuple val(meta), path("*.zip") , emit: zip optional true
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     // Calculate number of --cores for TrimGalore based on value of task.cpus
diff --git a/modules/nf-core/modules/ucsc/bedclip/main.nf b/modules/nf-core/modules/ucsc/bedclip/main.nf
index dacd72600..969a8f73e 100644
--- a/modules/nf-core/modules/ucsc/bedclip/main.nf
+++ b/modules/nf-core/modules/ucsc/bedclip/main.nf
@@ -17,6 +17,9 @@ process UCSC_BEDCLIP {
     tuple val(meta), path("*.bedGraph"), emit: bedgraph
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
index 9ba306aba..ef0ca088f 100644
--- a/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
@@ -17,6 +17,9 @@ process UCSC_BEDGRAPHTOBIGWIG {
     tuple val(meta), path("*.bigWig"), emit: bigwig
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/umitools/dedup/main.nf b/modules/nf-core/modules/umitools/dedup/main.nf
index ce21437db..1e46a6129 100644
--- a/modules/nf-core/modules/umitools/dedup/main.nf
+++ b/modules/nf-core/modules/umitools/dedup/main.nf
@@ -14,6 +14,9 @@ process UMITOOLS_DEDUP {
     tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/umitools/extract/main.nf b/modules/nf-core/modules/umitools/extract/main.nf
index fba8f0540..22a405b97 100644
--- a/modules/nf-core/modules/umitools/extract/main.nf
+++ b/modules/nf-core/modules/umitools/extract/main.nf
@@ -15,6 +15,9 @@ process UMITOOLS_EXTRACT {
     tuple val(meta), path("*.log")     , emit: log
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf
index 6d1996e77..01205e60d 100644
--- a/modules/nf-core/modules/untar/main.nf
+++ b/modules/nf-core/modules/untar/main.nf
@@ -14,6 +14,9 @@ process UNTAR {
     path "$untar"      , emit: untar
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''