nf-core modules bump-versions for all modules (#630)

* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests

.nf-core.yml

@@ -0,0 +1,9 @@
+bump-versions:
+  rseqc/junctionannotation: False
+  rseqc/bamstat: False
+  rseqc/readduplication: False
+  rseqc/readdistribution: False
+  rseqc/junctionsaturation: False
+  rseqc/inferexperiment: False
+  rseqc/innerdistance: False
+  sortmerna: False

modules/allelecounter/main.nf

@@ -11,11 +11,11 @@ process ALLELECOUNTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::cancerit-allelecount=4.2.1" : null)
+    conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.2.1--h3ecb661_0"
+        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
     } else {
-        container "quay.io/biocontainers/cancerit-allelecount:4.2.1--h3ecb661_0"
+        container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
     }
 
     input:

modules/bcftools/consensus/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_CONSENSUS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.11' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0'
+        container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
     } else {
-        container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
+        container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
     }
 
     input:

modules/bcftools/filter/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_FILTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/isec/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_ISEC {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/merge/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_MERGE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/mpileup/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_MPILEUP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/stats/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_STATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/blast/blastn/main.nf

@@ -11,11 +11,11 @@ process BLAST_BLASTN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
+    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
+        container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
     } else {
-        container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
+        container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
     }
 
     input:

modules/blast/makeblastdb/main.nf

@@ -11,11 +11,11 @@ process BLAST_MAKEBLASTDB {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
+    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
+        container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
     } else {
-        container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
+        container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
     }
 
     input:

modules/bowtie2/build/main.nf

@@ -11,11 +11,11 @@ process BOWTIE2_BUILD {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
+        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0'
     } else {
-        container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
+        container 'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0'
     }
 
     input:

modules/cnvkit/main.nf

@@ -11,11 +11,11 @@ process CNVKIT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::cnvkit=0.9.8" : null)
+    conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.8--py_0"
+        container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/cnvkit:0.9.8--py_0"
+        container "quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0"
     }
 
     input:

modules/cutadapt/main.nf

@@ -11,11 +11,11 @@ process CUTADAPT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::cutadapt=3.2' : null)
+    conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/cutadapt:3.2--py38h0213d0e_0'
+        container 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1'
     } else {
-        container 'quay.io/biocontainers/cutadapt:3.2--py38h0213d0e_0'
+        container 'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1'
     }
 
     input:

modules/deeptools/computematrix/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_COMPUTEMATRIX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotfingerprint/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTFINGERPRINT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotheatmap/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTHEATMAP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotprofile/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTPROFILE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/gubbins/main.nf

@@ -10,11 +10,11 @@ process GUBBINS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
+    conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
+        container "https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
+        container "quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0"
     }
 
     input:

modules/hisat2/build/main.nf

@@ -14,11 +14,11 @@ process HISAT2_BUILD {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
     } else {
-        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+        container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
     }
 
     input:

modules/hisat2/extractsplicesites/main.nf

@@ -13,11 +13,11 @@ process HISAT2_EXTRACTSPLICESITES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
     } else {
-        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+        container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
     }
 
     input:

modules/iqtree/main.nf

@@ -11,11 +11,11 @@ process IQTREE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::iqtree=2.1.2" : null)
+    conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/iqtree:2.1.2--h56fc30b_0"
+        container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
     } else {
-        container "quay.io/biocontainers/iqtree:2.1.2--h56fc30b_0"
+        container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
     }
 
     input:

modules/kallistobustools/count/main.nf

@@ -11,47 +11,45 @@ process KALLISTOBUSTOOLS_COUNT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
+    conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
+        container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
     }
 
     input:
-    tuple   val(meta),  path(reads)
+    tuple val(meta), path(reads)
-    path    index
+    path  index
-    path    t2g
+    path  t2g
-    path    t1c
+    path  t1c
-    path    t2c
+    path  t2c
-    val     use_t1c
+    val   workflow
-    val     use_t2c
+    val   technology
-    val     workflow
-    val     technology
 
     output:
-    tuple val(meta), path ("*_kallistobustools_count") , emit: kallistobustools_count
+    tuple val(meta), path ("*.count"), emit: count
-    path "*.version.txt"                               , emit: version
+    path "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def cdna  = use_t1c ? "-c1 $t1c" : ''
+    def cdna     = t1c ? "-c1 $t1c" : ''
-    def introns  = use_t2c ? "-c2 $t2c" : ''
+    def introns  = t2c ? "-c2 $t2c" : ''
     """
     kb \\
-    count \\
+        count \\
-    -t $task.cpus \\
+        -t $task.cpus \\
-    -i $index \\
+        -i $index \\
-    -g $t2g \\
+        -g $t2g \\
-    $cdna \\
+        $cdna \\
-    $introns \\
+        $introns \\
-    --workflow $workflow \\
+        --workflow $workflow \\
-    -x $technology \\
+        -x $technology \\
-    $options.args \\
+        $options.args \\
-    -o ${prefix}_kallistobustools_count \\
+        -o ${prefix}.count \\
-    ${reads[0]} \\
+        ${reads[0]} \\
-    ${reads[1]}
+        ${reads[1]}
 
     echo \$(kb 2>&1) | sed 's/^kb_python //; s/Usage.*\$//' > ${software}.version.txt
     """

modules/kallistobustools/count/meta.yml

@@ -18,14 +18,11 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - fastq1:
+  - reads:
-      type: file
+    type: file
-      description: Read 1 fastq file
+    description: |
-      pattern: "*.{fastq,fastq.gz}"
+      List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-  - fastq2:
+      respectively.
-      type: file
-      description: Read 2 fastq file
-      pattern: "*.{fastq,fastq.gz}"
   - index:
       type: file
       description: kb-ref index file (.idx)
@@ -38,17 +35,11 @@ input:
       type: file
       description: kb ref's c1 spliced_t2c file
       pattern: "*.{cdna_t2c.txt}"
-  - use_t1c:
-      type: boolean
-      description: Whether to use the c1 txt file for RNA velocity and nucleus workflows
   - t2c:
       type: file
       description: kb ref's c2 unspliced_t2c file
       pattern: "*.{introns_t2c.txt}"
-  - use_t2c:
+  - workflow:
-      type: boolean
-      description: Whether to use the c2 txt file for RNA velocity  and nucleus workflows
-  - kb_workflow:
       type: value
       description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
       pattern: "{standard,lamanno,nucleus,kite}"
@@ -57,17 +48,16 @@ input:
       description: String value defining the sequencing technology used.
       pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
 
-
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test']
-  - kallistobustools_count:
+  - count:
       type: file
       description: kb count output folder
-      pattern: "*_{kallistobustools_count}"
+      pattern: "*.{count}"
   - version:
       type: file
       description: File containing software version

modules/kallistobustools/ref/main.nf

@@ -11,11 +11,11 @@ process KALLISTOBUSTOOLS_REF {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
+    conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
+        container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
     }
 
     input:

modules/last/dotplot/main.nf

@@ -11,11 +11,11 @@ process LAST_DOTPLOT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/lastal/main.nf

@@ -11,11 +11,11 @@ process LAST_LASTAL {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/lastdb/main.nf

@@ -11,11 +11,11 @@ process LAST_LASTDB {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/mafconvert/main.nf

@@ -11,11 +11,11 @@ process LAST_MAFCONVERT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/mafswap/main.nf

@@ -11,11 +11,11 @@ process LAST_MAFSWAP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/postmask/main.nf

@@ -11,11 +11,11 @@ process LAST_POSTMASK {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/split/main.nf

@@ -11,11 +11,11 @@ process LAST_SPLIT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/train/main.nf

@@ -11,11 +11,11 @@ process LAST_TRAIN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::last=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/metaphlan3/main.nf

@@ -11,11 +11,11 @@ process METAPHLAN3 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::metaphlan=3.0.10" : null)
+    conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.10--pyhb7b1952_0"
+        container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0"
     } else {
-        container "quay.io/biocontainers/metaphlan:3.0.10--pyhb7b1952_0"
+        container "quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0"
     }
 
     input:

modules/methyldackel/extract/main.nf

@@ -11,11 +11,11 @@ process METHYLDACKEL_EXTRACT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::methyldackel=0.5.2" : null)
+    conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.2--h7435645_0"
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
     } else {
-        container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
+        container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
     }
 
     input:

modules/methyldackel/mbias/main.nf

@@ -11,11 +11,11 @@ process METHYLDACKEL_MBIAS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::methyldackel=0.5.2" : null)
+    conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.2--h7435645_0"
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
     } else {
-        container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
+        container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
     }
 
     input:

modules/minimap2/align/main.nf

@@ -11,11 +11,11 @@ process MINIMAP2_ALIGN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
+        container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+        container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
     }
 
     input:

modules/minimap2/index/main.nf

@@ -10,11 +10,11 @@ process MINIMAP2_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
 
-    conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
+        container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+        container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
     }
 
     input:

modules/mosdepth/main.nf

@@ -11,11 +11,11 @@ process MOSDEPTH {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::mosdepth=0.3.1' : null)
+    conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.1--ha7ba039_0"
+        container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
     } else {
-        container "quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_0"
+        container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
     }
 
     input:

modules/multiqc/main.nf

@@ -10,11 +10,11 @@ process MULTIQC {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/multiqc:1.10.1--py_0"
+        container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
     }
 
     input:

modules/nanoplot/main.nf

@@ -11,11 +11,11 @@ process NANOPLOT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::nanoplot=1.36.1" : null)
+    conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/nanoplot:1.36.1--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/nanoplot:1.36.1--pyhdfd78af_0"
+        container "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
     }
 
     input:

modules/picard/collectmultiplemetrics/main.nf

@@ -11,11 +11,11 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/collectwgsmetrics/main.nf

@@ -11,11 +11,11 @@ process PICARD_COLLECTWGSMETRICS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.25.0" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.25.0--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.25.0--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/filtersamreads/main.nf

@@ -11,11 +11,11 @@ process PICARD_FILTERSAMREADS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.25.6" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.25.6--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.25.6--hdfd78af_0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/markduplicates/main.nf

@@ -11,11 +11,11 @@ process PICARD_MARKDUPLICATES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/mergesamfiles/main.nf

@@ -11,11 +11,11 @@ process PICARD_MERGESAMFILES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/sortsam/main.nf

@@ -12,11 +12,11 @@ process PICARD_SORTSAM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::picard=2.25.6" : null)
+    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/picard:2.25.6--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.25.6--hdfd78af_0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/prodigal/meta.yml

@@ -1,32 +1,27 @@
 name: prodigal
-## TODO nf-core: Add a description of the module and list keywords
+description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
-description: write your description here
 keywords:
   - sort
 tools:
   - prodigal:
-      ## TODO nf-core: Add a description and other details for the software below
       description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
       homepage: {}
       documentation: {}
       tool_dev_url: {}
       doi: ""
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  ## TODO nf-core: Delete / customise this example input
   - bam:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   - meta:
       type: map
@@ -37,7 +32,6 @@ output:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"
-  ## TODO nf-core: Delete / customise this example output
   - bam:
       type: file
       description: Sorted BAM/CRAM/SAM file

modules/raxmlng/main.nf

@@ -10,11 +10,11 @@ process RAXMLNG {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::raxml-ng=1.0.2" : null)
+    conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.2--h7447c1b_0"
+        container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0"
     } else {
-        container "quay.io/biocontainers/raxml-ng:1.0.2--h7447c1b_0"
+        container "quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0"
     }
 
     input:

modules/salmon/index/main.nf

@@ -11,11 +11,11 @@ process SALMON_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
+    conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
+        container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
     } else {
-        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
+        container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
     }
 
     input:

modules/salmon/quant/main.nf

@@ -11,11 +11,11 @@ process SALMON_QUANT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
+    conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
+        container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
     } else {
-        container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
+        container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
     }
 
     input:

modules/samtools/faidx/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/fastq/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_FASTQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/flagstat/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_FLAGSTAT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/idxstats/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_IDXSTATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/index/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/merge/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/mpileup/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_MPILEUP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/sort/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_SORT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/stats/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_STATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/samtools/view/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_VIEW {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
     }
 
     input:

modules/seqkit/split2/main.nf

@@ -12,12 +12,12 @@ process SEQKIT_SPLIT2 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::seqkit=0.16.0" : null)
+    conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
 
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.16.0--h9ee0642_0"
+        container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
     } else {
-        container "quay.io/biocontainers/seqkit:0.16.0--h9ee0642_0"
+        container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
     }
 
     input:

modules/seqwish/induce/main.nf

@@ -12,12 +12,12 @@ process SEQWISH_INDUCE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::seqwish=0.4.1" : null)
+    conda (params.enable_conda ? 'bioconda::seqwish=0.7.1' : null)
 
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0"
+        container "https://depot.galaxyproject.org/singularity/seqwish:0.7.1--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
+        container "quay.io/biocontainers/seqwish:0.7.1--h2e03b76_0"
     }
 
     input:

modules/shovill/meta.yml

@@ -1,5 +1,4 @@
 name: shovill
-## TODO nf-core: Add a description of the module and list keywords
 description: Assemble bacterial isolate genomes from Illumina paired-end reads
 keywords:
   - bacterial
@@ -8,11 +7,10 @@ keywords:
 
 tools:
   - shovill:
-      ## TODO nf-core: Add a description and other details for the software below
       description: Microbial assembly pipeline for Illumina paired-end reads
       homepage: https://github.com/tseemann/shovill
       documentation: https://github.com/tseemann/shovill/blob/master/README.md
-      licence: ['GPL v2']
+      licence: ["GPL v2"]
 
 input:
   - meta:
@@ -21,8 +19,8 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - reads:
-        type: file
+      type: file
-        description: List of input paired-end FastQ files
+      description: List of input paired-end FastQ files
 
 output:
   - meta:

modules/spades/main.nf

@@ -11,11 +11,11 @@ process SPADES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
+    conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
+        container "https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0"
     } else {
-        container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
+        container "quay.io/biocontainers/spades:3.15.3--h95f258a_0"
     }
 
     input:

modules/tabix/bgzip/main.nf

@@ -11,11 +11,11 @@ process TABIX_BGZIP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
+    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
+        container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
+        container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
     }
 
     input:

modules/tabix/bgziptabix/main.nf

@@ -11,11 +11,11 @@ process TABIX_BGZIPTABIX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
+    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
+        container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
+        container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
     }
 
     input:

modules/tabix/tabix/main.nf

@@ -11,11 +11,11 @@ process TABIX_TABIX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
+    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
+        container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
+        container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
     }
 
     input:

modules/trimgalore/main.nf

@@ -11,11 +11,11 @@ process TRIMGALORE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
+    conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+        container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/trim-galore:0.6.6--0"
+        container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
     }
 
     input:

tests/modules/bcftools/filter/test.yml

@@ -5,4 +5,4 @@
     - bcftools
   files:
     - path: output/bcftools/test.vcf.gz
-      md5sum: 9d491cfa84067450342ba8e66c75e5b8
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2

tests/modules/bcftools/mpileup/test.yml

@@ -5,8 +5,8 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 2d506e32837a53a01fea0fc90402632a
+      md5sum: 74863ef525eef8d87e3119146d281bcf
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 11d90b5b35e4adf6b44fc53bec93bed3
+      md5sum: 0772419c5d819b4caa4aebfcad010c6e
     - path: output/bcftools/test.vcf.gz
-      md5sum: 2cf273a9fa3784383799b6b24df2f88c
+      md5sum: 9811674bb8da7ff30581319a910f2396

tests/modules/bcftools/stats/test.yml

@@ -5,4 +5,4 @@
     - bcftools/stats
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: c4c5938add12a20050eec3782c8ad623
+      md5sum: d3543531396cf7012f13ebdce639cbc8

tests/modules/blast/blastn/test.yml

@@ -13,10 +13,10 @@
     - path: ./output/blast/blast_db/genome.fasta.nhr
       md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
     - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 45f2daf9769957ff80868dd3d80d30a3
+      md5sum: 0d553c830656469211de113c5022f06d
     - path: ./output/blast/blast_db/genome.fasta.not
       md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
     - path: ./output/blast/blast_db/genome.fasta.nto
       md5sum: 33cdeccccebe80329f1fdbee7f5874cb
     - path: ./output/blast/blast_db/genome.fasta.ntf
-      md5sum: 1f6027d443e67a98ad0edc2d39971b0c
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb

tests/modules/blast/makeblastdb/test.yml

@@ -12,10 +12,10 @@
     - path: ./output/blast/blast_db/genome.fasta.nhr
       md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
     - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 45f2daf9769957ff80868dd3d80d30a3
+      md5sum: 0d553c830656469211de113c5022f06d
     - path: ./output/blast/blast_db/genome.fasta.not
       md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
     - path: ./output/blast/blast_db/genome.fasta.nto
       md5sum: 33cdeccccebe80329f1fdbee7f5874cb
     - path: ./output/blast/blast_db/genome.fasta.ntf
-      md5sum: 1f6027d443e67a98ad0edc2d39971b0c
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb

tests/modules/deeptools/plotfingerprint/test.yml

@@ -7,7 +7,7 @@
     - path: output/deeptools/test.plotFingerprint.pdf
     - path: output/deeptools/test.plotFingerprint.qcmetrics.txt
       contains:
-      - "AUC"
+        - "AUC"
-      - "0.24184576629880325"
+        - "0.24184576629880325"
     - path: output/deeptools/test.plotFingerprint.raw.txt
-      md5sum: e2a9ff341a315f49e7c8387a3323bdfb
+      md5sum: aff8e53de0ddd893aa9d8f9d4ce7e291

tests/modules/gubbins/test.yml

@@ -10,14 +10,14 @@
     - path: output/gubbins/all_sites.recombination_predictions.gff
       md5sum: f95871e79968340cb82532e2c9b0c92b
     - path: output/gubbins/all_sites.branch_base_reconstruction.embl
-      md5sum: 02e6fb268f7422bfe34b27ecd3b2c245
+      md5sum: 9e051646d630f528fff58f1f73286006
     - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
       md5sum: 276e62e888ea811577c8ffb2da0b3aff
     - path: output/gubbins/all_sites.per_branch_statistics.csv
-      md5sum: 94b09b25d10504b56aa0307beae98a98
+      md5sum: 25e4fdb6681c3709a9add1d5632bbf3e
     - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
       md5sum: 0a77f397a7797c5c3386832745b0c97a
     - path: output/gubbins/all_sites.final_tree.tre
-      md5sum: e3c7ea18e2c5c49774c0e2ff78bd1818
+      md5sum: 6cb251b58307aab11cb4b48792d6cda1
     - path: output/gubbins/all_sites.node_labelled.final_tree.tre
-      md5sum: 7727b4c4111ebf49cc8a4f1fdd25092c
+      md5sum: e01f965a15924b4f97603b8011c8d3f7

tests/modules/hisat2/align/test.yml

@@ -14,7 +14,7 @@
     - path: output/index/hisat2/genome.7.ht2
       md5sum: 9013eccd91ad614d7893c739275a394f
     - path: output/index/hisat2/genome.1.ht2
-      md5sum: 3ea3dc41304941ad8d047e4d71b4899e
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
     - path: output/index/hisat2/genome.2.ht2
       md5sum: 47b153cd1319abc88dda532462651fcf
     - path: output/index/hisat2/genome.6.ht2
@@ -42,7 +42,7 @@
     - path: output/index/hisat2/genome.7.ht2
       md5sum: 9013eccd91ad614d7893c739275a394f
     - path: output/index/hisat2/genome.1.ht2
-      md5sum: 3ea3dc41304941ad8d047e4d71b4899e
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
     - path: output/index/hisat2/genome.2.ht2
       md5sum: 47b153cd1319abc88dda532462651fcf
     - path: output/index/hisat2/genome.6.ht2

tests/modules/hisat2/build_test/test.yml

@@ -11,7 +11,7 @@
     - path: output/index/hisat2/genome.7.ht2
       md5sum: 9013eccd91ad614d7893c739275a394f
     - path: output/index/hisat2/genome.1.ht2
-      md5sum: 3ea3dc41304941ad8d047e4d71b4899e
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
     - path: output/index/hisat2/genome.2.ht2
       md5sum: 47b153cd1319abc88dda532462651fcf
     - path: output/index/hisat2/genome.6.ht2

tests/modules/kallistobustools/count/main.nf

@@ -5,20 +5,20 @@ nextflow.enable.dsl = 2
 include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
 
 workflow test_kallistobustools_count {
-    
-    input   = [ [id:'test_standard'], // meta map 
-                [file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_1.fastq.gz?raw=true", checkIfExists: true),
-                 file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_2.fastq.gz?raw=true", checkIfExists: true)] 
-                 ]  
-    
-    index       =   file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
-    t2g         =   file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
-    t1c         =   file('t1c_dummy')
-    t2c         =   file('t2c_dummy')
-    use_t1c     =   false
-    use_t2c     =   false
-    workflow    =   "standard"
-    technology  =   "10XV3"
 
-    KALLISTOBUSTOOLS_COUNT (input,index,t2g,t1c,t2c,use_t1c,use_t2c,workflow,technology)
+    input   = [
+        [id:'test'], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    index      = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
+    t2g        = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
+    t1c        = []
+    t2c        = []
+    workflow   = "standard"
+    technology = "10XV3"
+
+    KALLISTOBUSTOOLS_COUNT ( input, index, t2g, t1c, t2c, workflow, technology )
 }

tests/modules/kallistobustools/count/test.yml

@@ -4,33 +4,33 @@
     - kallistobustools/count
     - kallistobustools
   files:
-    - path: output/kallistobustools/test_standard_kallistobustools_count/10xv3_whitelist.txt
+    - path: output/kallistobustools/test.count/10x_version3_whitelist.txt
       md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/barcodes.tsv
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
       md5sum: 8f734732c46f52c4d1c025bfe4134bd2
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/genes.tsv
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
       md5sum: fbebf995a3de568db8ac028cd0c5d993
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/matrix.mtx
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
       md5sum: 4847bae27c41961496d504bcfe9890ba
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.barcodes.txt
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
       md5sum: cafdf96423987e3d9e807cdc16139541
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.genes.txt
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
       md5sum: 52d0627aaf0418bebe3ef75ad77da53f
-    - path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.mtx
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
       md5sum: d05e1582385ba5f215fa73c470343c06
-    - path: output/kallistobustools/test_standard_kallistobustools_count/inspect.json
+    - path: output/kallistobustools/test.count/inspect.json
       md5sum: d3d23063f3fc07f7fbd24748aa4271a9
-    - path: output/kallistobustools/test_standard_kallistobustools_count/kb_info.json
+    - path: output/kallistobustools/test.count/kb_info.json
-      contains: 
+      contains:
-      - 'kallisto'
+        - "kallisto"
-    - path: output/kallistobustools/test_standard_kallistobustools_count/matrix.ec
+    - path: output/kallistobustools/test.count/matrix.ec
       md5sum: cd8340e3fb78d74ad85fabdbe0a778f0
-    - path: output/kallistobustools/test_standard_kallistobustools_count/output.bus
+    - path: output/kallistobustools/test.count/output.bus
       md5sum: f4702922bd0c142e34b3680c2251426a
-    - path: output/kallistobustools/test_standard_kallistobustools_count/output.unfiltered.bus
+    - path: output/kallistobustools/test.count/output.unfiltered.bus
       md5sum: e38f99748e598e33fe035b89e7c89fb5
-    - path: output/kallistobustools/test_standard_kallistobustools_count/run_info.json
+    - path: output/kallistobustools/test.count/run_info.json
-      contains: 
+      contains:
-      - 'n_targets'
+        - "n_targets"
-    - path: output/kallistobustools/test_standard_kallistobustools_count/transcripts.txt
+    - path: output/kallistobustools/test.count/transcripts.txt
       md5sum: 6d583083eaf6ca81e409332a40d2e74c

tests/modules/kallistobustools/ref/test.yml

@@ -5,11 +5,8 @@
     - kallistobustools
   files:
     - path: output/kallistobustools/cdna.fa
-      md5sum: 0de7fdac9e7418576987ed93640927c7
     - path: output/kallistobustools/kb_ref_out.idx
-      md5sum: 7d5cd0731e7c467e5521d761f7d79895
     - path: output/kallistobustools/t2g.txt
-      md5sum: d5bcfd61ff078aa92e576abf8cc4fc08
 
 - name: kallistobustools ref test_kallistobustools_ref_lamanno
   command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
@@ -18,17 +15,11 @@
     - kallistobustools
   files:
     - path: output/kallistobustools/cdna.fa
-      md5sum: 0de7fdac9e7418576987ed93640927c7
     - path: output/kallistobustools/cdna_t2c.txt
-      md5sum: 6d583083eaf6ca81e409332a40d2e74c
     - path: output/kallistobustools/intron.fa
-      md5sum: ca5ca147afa0a25f6a730edfb39a6098
     - path: output/kallistobustools/intron_t2c.txt
-      md5sum: 728480007abfdbdb248f7ba9de6026ef
     - path: output/kallistobustools/kb_ref_out.idx
-      md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
     - path: output/kallistobustools/t2g.txt
-      md5sum: 7cae93dfb9a26f70adf4a57fe2a83027
 
 - name: kallistobustools ref test_kallistobustools_ref_nucleus
   command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
@@ -37,14 +28,8 @@
     - kallistobustools
   files:
     - path: output/kallistobustools/cdna.fa
-      md5sum: 0de7fdac9e7418576987ed93640927c7
     - path: output/kallistobustools/cdna_t2c.txt
-      md5sum: 6d583083eaf6ca81e409332a40d2e74c
     - path: output/kallistobustools/intron.fa
-      md5sum: ca5ca147afa0a25f6a730edfb39a6098
     - path: output/kallistobustools/intron_t2c.txt
-      md5sum: 728480007abfdbdb248f7ba9de6026ef
     - path: output/kallistobustools/kb_ref_out.idx
-      md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
     - path: output/kallistobustools/t2g.txt
-      md5sum: 7cae93dfb9a26f70adf4a57fe2a83027

tests/modules/last/lastal/test.yml

@@ -5,7 +5,7 @@
     - last/lastal
   files:
     - path: output/last/contigs.genome.maf.gz
-      md5sum: 2fc56553282d0826310bdef16a55e587
+      md5sum: 670f4fa1a94b23690cdb6fc603813c75
     - path: output/untar/lastdb/genome.bck
       md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
     - path: output/untar/lastdb/genome.des
@@ -28,7 +28,7 @@
     - last/lastal
   files:
     - path: output/last/contigs.genome.maf.gz
-      md5sum: f50557bed5430b42de7b0d5d61075cf0
+      md5sum: b0202b013e1caa9163516cd4ff4fbdbc
     - path: output/untar/lastdb/genome.bck
       md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
     - path: output/untar/lastdb/genome.des

tests/modules/last/lastdb/test.yml

@@ -9,7 +9,7 @@
     - path: output/last/lastdb/test.des
       md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
     - path: output/last/lastdb/test.prj
-      md5sum: 2c981eb9b9d2012d8413946a5b378f20
+      md5sum: 6948d17d2a10e470ea545f659930a543
     - path: output/last/lastdb/test.sds
       md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
     - path: output/last/lastdb/test.ssp
@@ -30,7 +30,7 @@
     - path: output/last/lastdb/test.des
       md5sum: 26ab49015cc572172b9efa50fc5190bc
     - path: output/last/lastdb/test.prj
-      md5sum: aec51a18da1c2361aaca70dd16eb7b7b
+      md5sum: d253fc4320d9b4d7fcfc43b2734412ee
     - path: output/last/lastdb/test.sds
       md5sum: cad9927d4bd161257e98165ad755d8e4
     - path: output/last/lastdb/test.ssp

tests/modules/minimap2/align/test.yml

@@ -5,7 +5,7 @@
     - minimap2/align
   files:
     - path: ./output/minimap2/test.paf
-      md5sum: 5a9648fc67c30a2c83b0ef094171faa0
+      md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
 
 - name: minimap2 align paired-end
   command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
@@ -14,4 +14,4 @@
     - minimap2/align
   files:
     - path: ./output/minimap2/test.paf
-      md5sum: e7b952be872bdbef16bf99d512690df7
+      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28

tests/modules/picard/markduplicates/test.yml

@@ -6,7 +6,7 @@
   files:
     - path: ./output/picard/test.MarkDuplicates.metrics.txt
     - path: ./output/picard/test.bam
-      md5sum: fe8ed25b4bd25be0cc7a8730fc3b2f30
+      md5sum: 3270bb142039e86aaf2ab83c540225d5
 
 - name: picard markduplicates on unsorted bam
   command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config

tests/modules/picard/mergesamfiles/test.yml

@@ -5,4 +5,4 @@
     - picard/mergesamfiles
   files:
     - path: ./output/picard/test.bam
-      md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb
+      md5sum: 82bb91735aff82eae4f0b631114e9e15

tests/modules/salmon/index/test.yml

@@ -8,7 +8,7 @@
     - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
     - path: ./output/index/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
     - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
     - path: ./output/index/salmon/mphf.bin

tests/modules/salmon/quant/test.yml

@@ -9,7 +9,7 @@
       md5sum: 687368b9963874c1797d210310b38516
     - path: ./output/salmon/test/lib_format_counts.json
     - path: ./output/salmon/test/quant.genes.sf
-      md5sum: ad4d31437f06db49b2436abeec29c78e
+      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
     - path: ./output/salmon/test/logs/salmon_quant.log
     - path: ./output/salmon/test/aux_info/expected_bias.gz
       md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
@@ -27,7 +27,7 @@
     - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
     - path: ./output/index/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
     - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
     - path: ./output/index/salmon/mphf.bin
@@ -60,7 +60,7 @@
       md5sum: 4abd35d0a60b5279b394424f0e6ea42d
     - path: ./output/salmon/test/lib_format_counts.json
     - path: ./output/salmon/test/quant.genes.sf
-      md5sum: d750f8c9f248e30c3a6d0c2678bf9c6a
+      md5sum: 29c8cd26f609cacd4fb88713df9c71c2
     - path: ./output/salmon/test/logs/salmon_quant.log
     - path: ./output/salmon/test/aux_info/expected_bias.gz
       md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
@@ -78,7 +78,7 @@
     - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
     - path: ./output/index/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
     - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
     - path: ./output/index/salmon/mphf.bin
@@ -112,7 +112,7 @@
       md5sum: 687368b9963874c1797d210310b38516
     - path: ./output/salmon/test/lib_format_counts.json
     - path: ./output/salmon/test/quant.genes.sf
-      md5sum: ad4d31437f06db49b2436abeec29c78e
+      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
     - path: ./output/salmon/test/logs/salmon_quant.log
     - path: output/salmon/test/aux_info/expected_bias.gz
       md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
@@ -130,7 +130,7 @@
     - path: output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
     - path: output/index/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
     - path: output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
     - path: output/index/salmon/mphf.bin

tests/modules/samtools/fastq/test.yml

@@ -5,6 +5,6 @@
     - samtools/fastq
   files:
     - path: output/samtools/test_2.fastq.gz
-      md5sum: 229daf1a62d114cae42c65801e8c0114
+      md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61
     - path: output/samtools/test_1.fastq.gz
-      md5sum: 4cab81f76e66361611621377f1b69d1d
+      md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9

tests/modules/samtools/flagstat/test.yml

@@ -5,4 +5,4 @@
     - samtools/flagstat
   files:
     - path: ./output/samtools/test.paired_end.sorted.bam.flagstat
-      md5sum: 6d7934c303b15ce473f64d502b79984e
+      md5sum: 4f7ffd1e6a5e85524d443209ac97d783

tests/modules/samtools/mpileup/test.yml

@@ -5,4 +5,4 @@
     - samtools/mpileup
   files:
     - path: ./output/samtools/test.mpileup
-      md5sum: 3608af83ffe3efbb1337f0ffb205337d
+      md5sum: 958e6bead4103d72026f80153b6b5150

tests/modules/samtools/sort/test.yml

@@ -5,4 +5,4 @@
     - samtools/sort
   files:
     - path: output/samtools/test.bam
-      md5sum: 3997667dee6b45d682865c6bf82d0378
+      md5sum: bdc2d9e3f579f84df1e242207b627f89

tests/modules/samtools/stats/test.yml

@@ -5,4 +5,4 @@
     - samtools/stats
   files:
     - path: ./output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: 95f7edae5d02c10c4004d9ab1d7d8ef3
+      md5sum: a7f36cf11fd3bf97e0a0ae29c0627296

tests/modules/spades/test.yml

@@ -4,11 +4,11 @@
     - spades
   files:
     - path: output/spades/test.assembly.gfa
-      md5sum: b2616d2beba83ab7d361b54778d1e759
+      md5sum: a995d1d413031534180d2b3b715fa921
     - path: output/spades/test.contigs.fa
-      md5sum: 2690fefde046bc904e90df09a065257a
+      md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
     - path: output/spades/test.scaffolds.fa
-      md5sum: 2690fefde046bc904e90df09a065257a
+      md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
     - path: output/spades/test.spades.log
 
 - name: spades paired end
@@ -17,7 +17,7 @@
     - spades
   files:
     - path: output/spades/test.assembly.gfa
-      md5sum: faf76135ee390606b899c0197dc38e04
+      md5sum: bb053ef4e9250829c980ca17fbdbe3e9
     - path: output/spades/test.contigs.fa
-      md5sum: 6148e25b33890c80f176f90f2dd88989
+      md5sum: 4476d409da70d9f7fc2aa8f25bbaf7fd
     - path: output/spades/test.spades.log

tests/modules/tabix/bgzip/test.yml

@@ -5,4 +5,4 @@
     - tabix/bgzip
   files:
     - path: ./output/tabix/test.vcf.gz
-      md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2

tests/modules/tabix/bgziptabix/test.yml

@@ -5,6 +5,6 @@
     - tabix/bgziptabix
   files:
     - path: ./output/tabix/test.gz
-      md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
     - path: ./output/tabix/test.gz.tbi
-      md5sum: bbec39fd53cf2834909d52094980d094
+      md5sum: 36e11bf96ed0af4a92caa91a68612d64

tests/modules/tabix/tabix/test.yml

@@ -5,7 +5,7 @@
     - tabix/tabix
   files:
     - path: ./output/tabix/test.bed.gz.tbi
-      md5sum: 115922d881d24879b15d20c3734495ac
+      md5sum: 5b40851ab6b8ccf7946313c86481c0df
 - name: tabix tabix gff
   command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
   tags:
@@ -13,7 +13,7 @@
     - tabix/tabix
   files:
     - path: ./output/tabix/genome.gff3.gz.tbi
-      md5sum: 4059fe4762568194cf293fc6df7b358b
+      md5sum: f79a67d95a98076e04fbe0455d825926
 - name: tabix tabix vcf
   command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
   tags:
@@ -21,4 +21,4 @@
     - tabix/tabix
   files:
     - path: output/tabix/test.vcf.gz.tbi
-      md5sum: bbec39fd53cf2834909d52094980d094
+      md5sum: 36e11bf96ed0af4a92caa91a68612d64