From a547f27f2181c821d09b1caf5a47414c03c4759f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:41:31 +0200
Subject: [PATCH 1/7] New GitHub Action to lint code style

---
 .github/workflows/lint-code.yml | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 .github/workflows/lint-code.yml

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
new file mode 100644
index 00000000..df26d0b0
--- /dev/null
+++ b/.github/workflows/lint-code.yml
@@ -0,0 +1,53 @@
+name: Lint Code
+on: [push, pull_request]
+
+jobs:
+  Markdown:
+    name: Test Markdown syntax
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+
+      - name: Install markdownlint
+        run: npm install -g markdownlint-cli
+
+      - name: Run Markdownlint
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+  EditorConfig:
+    name: Test Editor Config rules
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+
+      - name: Install ECLint
+        run: npm install -g eclint
+
+      - name: Run ECLint check
+        run: eclint check $(git ls-files | grep -v test)
+
+  YAML:
+    name: Test YAML syntax
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v1
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+
+      - name: Install yaml-lint
+        run: npm install -g yaml-lint
+
+      - name: Run yaml-lint
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")

From ae38a9bf4164f502a113c1fadabd1e9474cbb595 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:42:13 +0200
Subject: [PATCH 2/7] Fix editor config styles

---
 .gitmodules                   |  4 +-
 README.md                     |  2 +-
 tools/bowtie2/main.nf         | 74 +++++++++++++++++------------------
 tools/bowtie2/meta.yml        |  2 +-
 tools/bwa/index/main.nf       |  2 +-
 tools/bwa/mem/Dockerfile      |  4 +-
 tools/cutadapt/main.nf        | 28 ++++++-------
 tools/cutadapt/meta.yml       |  6 +--
 tools/fastq_screen/main.nf    | 54 ++++++++++++-------------
 tools/fastqc/Dockerfile       |  2 +-
 tools/fastqc/main.nf          | 44 ++++++++++-----------
 tools/fastqc/meta.yml         |  2 +-
 tools/gatk/dict/main.nf       |  2 +-
 tools/gatk/dict/meta.yml      |  2 +-
 tools/hisat2/main.nf          |  8 ++--
 tools/hisat2/meta.yml         |  2 +-
 tools/htslib/tabix/meta.yml   |  2 +-
 tools/multiqc/main.nf         | 32 +++++++--------
 tools/samtools/Dockerfile     |  2 +-
 tools/samtools/faidx/meta.yml |  2 +-
 tools/shovill/main.nf         |  4 +-
 tools/tcoffee/main.nf         |  1 -
 tools/trim_galore/Dockerfile  |  2 +-
 tools/trim_galore/main.nf     | 65 +++++++++++++++---------------
 tools/trim_galore/meta.yml    |  2 +-
 tools/umi_tools/Dockerfile    |  4 +-
 tools/umi_tools/main.nf       |  2 +-
 tools/umi_tools/umi_tools.yml |  7 ++--
 28 files changed, 179 insertions(+), 184 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 15bfef35..44e06649 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "test-datasets"]
-	path = test-datasets
-	url = https://github.com/nf-core/test-datasets.git
+    path = test-datasets
+    url = https://github.com/nf-core/test-datasets.git
diff --git a/README.md b/README.md
index 276f8943..7730d9c7 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ The features offered by Nextflow DSL 2 can be used in various ways depending on
 
 * *Module*: A `process`that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as `FastQC`. This repository has been created to only host atomic module files that should be added to the `tools` sub-directory along with the required documentation, software and tests.
 * *Sub-workflow*: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline.  For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows.
-* *Workflow*: What DSL 1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL 1, or by using a combination of DSL 2 individual modules and sub-workflows. 
+* *Workflow*: What DSL 1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL 1, or by using a combination of DSL 2 individual modules and sub-workflows.
 
 ## Using existing modules
 
diff --git a/tools/bowtie2/main.nf b/tools/bowtie2/main.nf
index 6d1dc55e..467a5761 100644
--- a/tools/bowtie2/main.nf
+++ b/tools/bowtie2/main.nf
@@ -2,51 +2,51 @@ nextflow.preview.dsl=2
 params.genome = ''
 
 process BOWTIE2 {
-	// depending on the genome used one might want/need to adjust the memory settings.
-	// For the E. coli test data this is probably not required
+    // depending on the genome used one might want/need to adjust the memory settings.
+    // For the E. coli test data this is probably not required
+
+    // label 'bigMem'
+    // label 'multiCore'
 
-	// label 'bigMem' 
-	// label 'multiCore'
-		
     input:
-	    tuple val(name), path(reads)
-		val (outdir)
-		val (bowtie2_args)
-		val (verbose)
+        tuple val(name), path(reads)
+        val (outdir)
+        val (bowtie2_args)
+        val (verbose)
 
-	output:
-	    path "*bam",  emit: bam
-		path "*stats.txt", emit: stats 
+    output:
+        path "*bam",  emit: bam
+        path "*stats.txt", emit: stats
 
-	publishDir "$outdir/bowtie2",
-		mode: "copy", overwrite: true
+    publishDir "$outdir/bowtie2",
+        mode: "copy", overwrite: true
 
-	script:
-		if (verbose){
-			println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
-		}
+    script:
+        if (verbose){
+            println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
+        }
 
-		cores = 4
+        cores = 4
 
-		readString = ""
+        readString = ""
 
-		// Options we add are
-		bowtie2_options = bowtie2_args
-		bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
-		
-		// single-end / paired-end distinction. Might also be handled via params.single_end 
-		if (reads instanceof List) {
-			readString = "-1 " + reads[0] + " -2 " + reads[1]
-		}
-		else {
-			readString = "-U " + reads
-		}
-		
-		index = params.genome["bowtie2"]
-		bowtie2_name = name + "_" + params.genome["name"]
+        // Options we add are
+        bowtie2_options = bowtie2_args
+        bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
 
-		"""
-		bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
-		"""
+        // single-end / paired-end distinction. Might also be handled via params.single_end
+        if (reads instanceof List) {
+            readString = "-1 " + reads[0] + " -2 " + reads[1]
+        }
+        else {
+            readString = "-U " + reads
+        }
+
+        index = params.genome["bowtie2"]
+        bowtie2_name = name + "_" + params.genome["name"]
+
+        """
+        bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
+        """
 
 }
diff --git a/tools/bowtie2/meta.yml b/tools/bowtie2/meta.yml
index b3b31a94..f30ee823 100644
--- a/tools/bowtie2/meta.yml
+++ b/tools/bowtie2/meta.yml
@@ -1,4 +1,4 @@
-name: Bowtie 2 
+name: Bowtie 2
 description: Ultrafast alignment to reference genome
 keywords:
     - Alignment
diff --git a/tools/bwa/index/main.nf b/tools/bwa/index/main.nf
index 0c943bb4..051ed70e 100644
--- a/tools/bwa/index/main.nf
+++ b/tools/bwa/index/main.nf
@@ -13,4 +13,4 @@ process bwa_index {
     """
     bwa index ${fasta}
     """
-}
\ No newline at end of file
+}
diff --git a/tools/bwa/mem/Dockerfile b/tools/bwa/mem/Dockerfile
index 0be4dc78..9a3e0caa 100644
--- a/tools/bwa/mem/Dockerfile
+++ b/tools/bwa/mem/Dockerfile
@@ -1,9 +1,7 @@
 FROM nfcore/base
 LABEL authors="Jeremy Guntoro" \
-      description="Docker image containing all requirements for nf-core/modules/bwa/mem module"
+    description="Docker image containing all requirements for nf-core/modules/bwa/mem module"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH /opt/conda/envs/nf-core-bwa-mem/bin:$PATH
-
-
diff --git a/tools/cutadapt/main.nf b/tools/cutadapt/main.nf
index bdd444af..734b30b1 100644
--- a/tools/cutadapt/main.nf
+++ b/tools/cutadapt/main.nf
@@ -13,27 +13,27 @@ process cutadapt {
     forward_fq = "trimmed_1.fastq"
     reverse_fq = "trimmed_2.fastq"
 
-    
+
     if (params.singleEnd) {
         processing = """
                     cutadapt \
-		            	-j ${task.cpus} \
-		            	-q $params.cutadapt_min_quality \
-		            	--minimum-length $params.cutadapt_min_length \
-		            	--output ${forward_fq} \
-		            	${reads}
+                        -j ${task.cpus} \
+                        -q $params.cutadapt_min_quality \
+                        --minimum-length $params.cutadapt_min_length \
+                        --output ${forward_fq} \
+                        ${reads}
                     """
     } else {
         processing = """
                     cutadapt \
-		            	-j ${task.cpus} \
-		            	-q $params.cutadapt_min_quality \
-		            	--minimum-length $params.cutadapt_min_length \
-		            	--pair-filter=any \
-		            	--output ${forward_fq} \
-		            	--paired-output ${reverse_fq} ${reads}
-            
-                    
+                        -j ${task.cpus} \
+                        -q $params.cutadapt_min_quality \
+                        --minimum-length $params.cutadapt_min_length \
+                        --pair-filter=any \
+                        --output ${forward_fq} \
+                        --paired-output ${reverse_fq} ${reads}
+
+
                     """
     }
 
diff --git a/tools/cutadapt/meta.yml b/tools/cutadapt/meta.yml
index 8df0b244..bb3bb8a8 100644
--- a/tools/cutadapt/meta.yml
+++ b/tools/cutadapt/meta.yml
@@ -9,10 +9,10 @@ tools:
         description: |
             Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence
             from your high-throughput sequencing reads.
-            
+
             Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’
-            sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads 
-            start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but 
+            sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads
+            start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but
             often you don’t want them to be in your reads.
         homepage: https://cutadapt.readthedocs.io/en/stable/
         documentation: https://cutadapt.readthedocs.io/en/stable/
diff --git a/tools/fastq_screen/main.nf b/tools/fastq_screen/main.nf
index be088ff5..2eccf31f 100644
--- a/tools/fastq_screen/main.nf
+++ b/tools/fastq_screen/main.nf
@@ -1,38 +1,38 @@
 nextflow.preview.dsl=2
 
 process FASTQ_SCREEN {
-	
-	// depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
-	// label 'bigMem'
-	// label 'multiCore'
+
+    // depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
+    // label 'bigMem'
+    // label 'multiCore'
 
     input:
-	    tuple val(name), path(reads)
-		val (outputdir)
-		// fastq_screen_args are best passed in to the workflow in the following manner:
-		// --fastq_screen_args="--subset 200000 --force"
-		val (fastq_screen_args)  
-		val (verbose)
+        tuple val(name), path(reads)
+        val (outputdir)
+        // fastq_screen_args are best passed in to the workflow in the following manner:
+        // --fastq_screen_args="--subset 200000 --force"
+        val (fastq_screen_args)
+        val (verbose)
 
-	output:
-	    path "*png",  emit: png
-	    path "*html", emit: html
-		path "*txt",  emit: report
+    output:
+        path "*png",  emit: png
+        path "*html", emit: html
+        path "*txt",  emit: report
 
-	publishDir "$outputdir",
-		mode: "link", overwrite: true
+    publishDir "$outputdir",
+        mode: "link", overwrite: true
 
     script:
-		println(name)
-		println(reads)
-		println(outputdir)
-		if (verbose){
-			println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
-		}
+        println(name)
+        println(reads)
+        println(outputdir)
+        if (verbose){
+            println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
+        }
 
-	"""
-	module load fastq_screen
-	fastq_screen $fastq_screen_args $reads
-	"""
+    """
+    module load fastq_screen
+    fastq_screen $fastq_screen_args $reads
+    """
 
-}
\ No newline at end of file
+}
diff --git a/tools/fastqc/Dockerfile b/tools/fastqc/Dockerfile
index a6f4f8ce..5bfca1b9 100644
--- a/tools/fastqc/Dockerfile
+++ b/tools/fastqc/Dockerfile
@@ -1,6 +1,6 @@
 FROM nfcore/base:1.7
 LABEL authors="phil.ewels@scilifelab.se" \
-      description="Docker image for nf-core modules fastqc"
+    description="Docker image for nf-core modules fastqc"
 
 # foobar
 COPY environment.yml /
diff --git a/tools/fastqc/main.nf b/tools/fastqc/main.nf
index 83956ae8..3ecf31ed 100644
--- a/tools/fastqc/main.nf
+++ b/tools/fastqc/main.nf
@@ -1,37 +1,37 @@
 nextflow.preview.dsl = 2
 
-process FASTQC {	
-    
+process FASTQC {
+
     // tag "FastQC - $sample_id"
 
-	input:
-	    tuple val(name), path(reads)
-		val (outputdir)
+    input:
+        tuple val(name), path(reads)
+        val (outputdir)
         // fastqc_args are best passed into the workflow in the following manner:
         // --fastqc_args="--nogroup -a custom_adapter_file.txt"
-		val (fastqc_args)
-		val (verbose)
+        val (fastqc_args)
+        val (verbose)
 
-	output:
-	    tuple val(name), path ("*fastqc*"), emit: all
-		path "*.zip",                       emit: report // e.g. for MultiQC later
-	
-    // container 'quay.io/biocontainers/fastqc:0.11.8--2' 
+    output:
+        tuple val(name), path ("*fastqc*"), emit: all
+        path "*.zip",                       emit: report // e.g. for MultiQC later
 
-	publishDir "$outputdir",
-		mode: "copy", overwrite: true
+    // container 'quay.io/biocontainers/fastqc:0.11.8--2'
 
-	script:
+    publishDir "$outputdir",
+        mode: "copy", overwrite: true
 
-		if (verbose){
-			println ("[MODULE] FASTQC ARGS: " + fastqc_args)
-		}
+    script:
 
-		"""
-		module load fastqc
-		fastqc $fastqc_args -q -t 2 $reads
+        if (verbose){
+            println ("[MODULE] FASTQC ARGS: " + fastqc_args)
+        }
+
+        """
+        module load fastqc
+        fastqc $fastqc_args -q -t 2 $reads
 
         fastqc --version &> fastqc.version.txt
-		"""
+        """
 
 }
diff --git a/tools/fastqc/meta.yml b/tools/fastqc/meta.yml
index 0d67f866..bfe0f6cf 100644
--- a/tools/fastqc/meta.yml
+++ b/tools/fastqc/meta.yml
@@ -29,6 +29,6 @@ output:
             description: FastQC report
             pattern: *_fastqc.{zip,html}
 authors:
-    - 
+    -
         - @ewels
         - @FelixKrueger
diff --git a/tools/gatk/dict/main.nf b/tools/gatk/dict/main.nf
index 49edf5a1..9de2e2f8 100644
--- a/tools/gatk/dict/main.nf
+++ b/tools/gatk/dict/main.nf
@@ -16,4 +16,4 @@ process gatk_dict {
         --REFERENCE ${fasta} \
         --OUTPUT ${fasta.baseName}.dict
     """
-}
\ No newline at end of file
+}
diff --git a/tools/gatk/dict/meta.yml b/tools/gatk/dict/meta.yml
index bc9e18b6..527d6a69 100644
--- a/tools/gatk/dict/meta.yml
+++ b/tools/gatk/dict/meta.yml
@@ -22,4 +22,4 @@ output:
             description: gatk dictionary file
             pattern: *.{fasta,fa}.{dict}
 authors:
-    - @maxulysse
\ No newline at end of file
+    - @maxulysse
diff --git a/tools/hisat2/main.nf b/tools/hisat2/main.nf
index 55e6fe78..85baa120 100644
--- a/tools/hisat2/main.nf
+++ b/tools/hisat2/main.nf
@@ -15,17 +15,17 @@ process HISAT2 {
 
     output:
         path "*bam",       emit: bam
-        path "*stats.txt", emit: stats 
+        path "*stats.txt", emit: stats
 
     publishDir "$outdir/hisat2",
         mode: "copy", overwrite: true
 
     script:
-    
+
         if (verbose){
             println ("[MODULE] HISAT2 ARGS: " + hisat2_args)
         }
-    
+
         cores = 4
         readString = ""
         hisat_options = hisat2_args
@@ -41,7 +41,7 @@ process HISAT2 {
             readString = "-U "+reads
         }
         index = params.genome["hisat2"]
-        
+
         splices = ''
         if (params.genome.containsKey("hisat2_splices")){
             splices = " --known-splicesite-infile " + params.genome["hisat2_splices"]
diff --git a/tools/hisat2/meta.yml b/tools/hisat2/meta.yml
index ee79ba99..d5f5e403 100644
--- a/tools/hisat2/meta.yml
+++ b/tools/hisat2/meta.yml
@@ -1,4 +1,4 @@
-name: HISAT2 
+name: HISAT2
 description: Graph-based alignment of next generation sequencing reads to a population of genomes
 keywords:
     - Alignment
diff --git a/tools/htslib/tabix/meta.yml b/tools/htslib/tabix/meta.yml
index 027780c3..d35ec2f2 100644
--- a/tools/htslib/tabix/meta.yml
+++ b/tools/htslib/tabix/meta.yml
@@ -23,4 +23,4 @@ output:
             description: tabix index file
             pattern: *.{vcf.gz.tbi}
 authors:
-    - @maxulysse
\ No newline at end of file
+    - @maxulysse
diff --git a/tools/multiqc/main.nf b/tools/multiqc/main.nf
index 493497c1..ab932a2f 100644
--- a/tools/multiqc/main.nf
+++ b/tools/multiqc/main.nf
@@ -1,31 +1,31 @@
 nextflow.preview.dsl=2
 
 process MULTIQC {
-	
+
     // tag "FastQC - $sample_id"
-    
+
     input:
-	    path (file)
-		val (outdir)
-		val (multiqc_args)
+        path (file)
+        val (outdir)
+        val (multiqc_args)
         // multiqc_args are best passed into the workflow in the following manner:
         // --multiqc_args="--exlude STAR --title custom_report_title"
-		val (verbose)
+        val (verbose)
 
-	output:
-	    path "*html",       emit: html
+    output:
+        path "*html",       emit: html
 
-	publishDir "${outdir}/multiqc",
-		mode: "copy", overwrite: true
+    publishDir "${outdir}/multiqc",
+        mode: "copy", overwrite: true
 
     script:
 
-		if (verbose){
-			println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
-		}
+        if (verbose){
+            println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
+        }
 
-		"""
-		multiqc $multiqc_args -x work . 
-		"""
+        """
+        multiqc $multiqc_args -x work .
+        """
 
 }
diff --git a/tools/samtools/Dockerfile b/tools/samtools/Dockerfile
index 3d5cf586..ff8c7c64 100644
--- a/tools/samtools/Dockerfile
+++ b/tools/samtools/Dockerfile
@@ -1,6 +1,6 @@
 FROM nfcore/base:1.7
 LABEL authors="phil.ewels@scilifelab.se" \
-      description="Docker image for nf-core modules samtools"
+    description="Docker image for nf-core modules samtools"
 
 # foobar
 COPY environment.yml /
diff --git a/tools/samtools/faidx/meta.yml b/tools/samtools/faidx/meta.yml
index 1e402057..777eb051 100644
--- a/tools/samtools/faidx/meta.yml
+++ b/tools/samtools/faidx/meta.yml
@@ -24,4 +24,4 @@ output:
             description: samtools index fasta file
             pattern: *.fasta.fai
 authors:
-    - @maxulysse
\ No newline at end of file
+    - @maxulysse
diff --git a/tools/shovill/main.nf b/tools/shovill/main.nf
index cf52ba10..5c6a3ee5 100644
--- a/tools/shovill/main.nf
+++ b/tools/shovill/main.nf
@@ -3,7 +3,7 @@ process shovill {
     tag { shovill }
 
     publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'
-  
+
     container "quay.io/biocontainers/shovill:1.0.9--0"
 
     input:
@@ -11,7 +11,7 @@ process shovill {
 
     output:
     path("${sample_id}.fasta")
-   
+
     script:
     """
     shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
diff --git a/tools/tcoffee/main.nf b/tools/tcoffee/main.nf
index 42945850..5d863a7d 100644
--- a/tools/tcoffee/main.nf
+++ b/tools/tcoffee/main.nf
@@ -14,4 +14,3 @@ process tcoffee {
     t_coffee -seq $fasta -outfile ${fasta}.aln
     """
 }
-
diff --git a/tools/trim_galore/Dockerfile b/tools/trim_galore/Dockerfile
index 56f75baa..ef13a1bf 100644
--- a/tools/trim_galore/Dockerfile
+++ b/tools/trim_galore/Dockerfile
@@ -1,6 +1,6 @@
 FROM nfcore/base:1.7
 LABEL authors="phil.ewels@scilifelab.se" \
-      description="Docker image for nf-core modules trimgalore"
+    description="Docker image for nf-core modules trimgalore"
 
 # foobar
 COPY environment.yml /
diff --git a/tools/trim_galore/main.nf b/tools/trim_galore/main.nf
index 3a4e8496..eedbe896 100644
--- a/tools/trim_galore/main.nf
+++ b/tools/trim_galore/main.nf
@@ -13,43 +13,43 @@ params.three_prime_clip_r1 = 0
 params.three_prime_clip_r2 = 0
 
 
-process TRIM_GALORE {	
-    
+process TRIM_GALORE {
+
     // container 'quay.io/biocontainers/trim-galore:0.6.5--0' // maybe later
     // tag "$sample_id"
 
-	input:
-	    tuple val (name), path (reads)
-		val (outdir)
-		val (trim_galore_args)
-		val (verbose)
+    input:
+        tuple val (name), path (reads)
+        val (outdir)
+        val (trim_galore_args)
+        val (verbose)
+
+    output:
+        tuple val(name), path ("*fq.gz"),             emit: reads
+        path "*trimming_report.txt", optional: true,  emit: report
 
-	output:
-	    tuple val(name), path ("*fq.gz"),             emit: reads
-		path "*trimming_report.txt", optional: true,  emit: report
-		
         // Trimming reports are not generated for e.g. --hardtrim5, --clock etc
         // saveAs: {filename ->
         //   else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
         //   else filename
         // }
 
-	publishDir "${outdir}/trim_galore",
-		mode: "copy", overwrite: true
+    publishDir "${outdir}/trim_galore",
+        mode: "copy", overwrite: true
 
     script:
-		if (verbose){
-			println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
-		}
-		
+        if (verbose){
+            println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
+        }
+
         trim_galore_args += " --gzip "           // we like small files
 
-		pairedString = 0
-		if (reads instanceof List) {
-			pairedString = 1
+        pairedString = 0
+        if (reads instanceof List) {
+            pairedString = 1
             trim_galore_args += " --paired "
-		}
-		
+        }
+
         if (params.clip_r1 > 0){
             trim_galore_args += " --clip_r1 ${params.clip_r1} "
         }
@@ -62,12 +62,12 @@ process TRIM_GALORE {
         if (params.three_prime_clip_r2 > 0){
             trim_galore_args += " --three_prime_clip_r2 ${params.three_prime_clip_r2} "
         }
-        
+
         if (params.trim_nextseq > 0){
             trim_galore_args += " --nextseq ${params.trim_nextseq} "
-        }   
-    
-        
+        }
+
+
         // Pre-set parameters for certain bisulfite-seq applications
         if (params.singlecell){
             trim_galore_args += " --clip_r1 6 "
@@ -77,7 +77,7 @@ process TRIM_GALORE {
         }
         if (params.rrbs){
             trim_galore_args += " --rrbs "
-        } 
+        }
         if  (params.pbat){
             trim_galore_args += " --clip_r1 $params.pbat "
             if (pairedString == 1){
@@ -85,17 +85,16 @@ process TRIM_GALORE {
             }
         }
 
-		"""
-		module load trim_galore
-		trim_galore $trim_galore_args $reads
-		"""
+        """
+        module load trim_galore
+        trim_galore $trim_galore_args $reads
+        """
 
 }
 
 
 
- 
 
 
-  
+
 
diff --git a/tools/trim_galore/meta.yml b/tools/trim_galore/meta.yml
index d6944fb6..b3d42f81 100644
--- a/tools/trim_galore/meta.yml
+++ b/tools/trim_galore/meta.yml
@@ -36,6 +36,6 @@ output:
             pattern: *trimming_report.txt
 
 authors:
-    - 
+    -
         - @ewels
         - @FelixKrueger
diff --git a/tools/umi_tools/Dockerfile b/tools/umi_tools/Dockerfile
index 691f576f..19a390f3 100644
--- a/tools/umi_tools/Dockerfile
+++ b/tools/umi_tools/Dockerfile
@@ -1,8 +1,8 @@
 FROM nfcore/base:1.7
 LABEL authors="chris.cheshire@crick.ac.uk" \
-      description="Docker image containing all requirements for the nf-core umi_tools module"
+    description="Docker image containing all requirements for the nf-core umi_tools module"
 
 # Install conda packages
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nfcore-module-umitools/bin:$PATH
\ No newline at end of file
+ENV PATH /opt/conda/envs/nfcore-module-umitools/bin:$PATH
diff --git a/tools/umi_tools/main.nf b/tools/umi_tools/main.nf
index 049ceaf8..b3c89a97 100644
--- a/tools/umi_tools/main.nf
+++ b/tools/umi_tools/main.nf
@@ -12,7 +12,7 @@ process umitools_dedup {
 
     input:
         tuple val(sample_id), path(bam)
-       
+
     output:
         tuple val(sample_id), path("${sample_id}.dedup.bam"), emit: dedupBam
         tuple val(sample_id), path("${sample_id}.dedup.bam.bai"), emit: dedupBai
diff --git a/tools/umi_tools/umi_tools.yml b/tools/umi_tools/umi_tools.yml
index 64bcb6aa..b04f0f4e 100644
--- a/tools/umi_tools/umi_tools.yml
+++ b/tools/umi_tools/umi_tools.yml
@@ -1,6 +1,6 @@
 name: umi_tools
 version: 1.0
-description: Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. 
+description: Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
 keywords:
     - UMI
     - RMT
@@ -8,7 +8,7 @@ keywords:
 tools:
     - umi_tools:
         description: |
-            Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. 
+            Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
         homepage: https://github.com/CGATOxford/UMI-tools
         documentation: https://umi-tools.readthedocs.io/en/latest/
 processes:
@@ -18,7 +18,7 @@ processes:
             The program will execute with the following pattern:
                 umi_tools dedup --log={SAMPLE_ID}.dedup.log {params.umitools_dedup_args} -I {SAMPLE_ID}.bam -S {SAMPLE_ID}.dedup.bam --output-stats={SAMPLE_ID}
         description: |
-            Groups PCR duplicates and de-duplicates reads to yield one read per group. 
+            Groups PCR duplicates and de-duplicates reads to yield one read per group.
             Use this when you want to remove the PCR duplicates prior to any downstream analysis.
         input:
             - sample_id:
@@ -43,4 +43,3 @@ processes:
 authors:
     - @candiceh08
     - @chris-cheshire
-

From fc53a6f0b5e4d2b3bfe24cc41a06420ced1d8df7 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:44:28 +0200
Subject: [PATCH 3/7] Added markdown lint config file

---
 .github/markdownlint.yml | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 .github/markdownlint.yml

diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
new file mode 100644
index 00000000..e052a635
--- /dev/null
+++ b/.github/markdownlint.yml
@@ -0,0 +1,9 @@
+# Markdownlint configuration file
+default: true,
+line-length: false
+no-multiple-blanks: 0
+blanks-around-headers: false
+blanks-around-lists: false
+header-increment: false
+no-duplicate-header:
+    siblings_only: true

From 45fb2ff4f4284b6eedd304e462f625227a473a34 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:45:08 +0200
Subject: [PATCH 4/7] Remove verbose job names

---
 .github/workflows/lint-code.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index df26d0b0..fb9385c7 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -3,7 +3,6 @@ on: [push, pull_request]
 
 jobs:
   Markdown:
-    name: Test Markdown syntax
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -19,7 +18,6 @@ jobs:
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
 
   EditorConfig:
-    name: Test Editor Config rules
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -35,7 +33,6 @@ jobs:
         run: eclint check $(git ls-files | grep -v test)
 
   YAML:
-    name: Test YAML syntax
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository

From 263f48d5203054c7a4305282d667a807bbb3ded3 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:48:11 +0200
Subject: [PATCH 5/7] Fix markdownlint

---
 .github/markdownlint.yml | 2 ++
 README.md                | 1 +
 2 files changed, 3 insertions(+)

diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
index e052a635..9d1a3083 100644
--- a/.github/markdownlint.yml
+++ b/.github/markdownlint.yml
@@ -7,3 +7,5 @@ blanks-around-lists: false
 header-increment: false
 no-duplicate-header:
     siblings_only: true
+ul-indent:
+  indent: 4
diff --git a/README.md b/README.md
index 7730d9c7..74f5115a 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,7 @@
 A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl2.htmlhttps://www.nextflow.io/docs/edge/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
 
 ## Table of contents
+
 * [Using existing modules](#using-existing-modules)
     * [Configuration and parameters](#configuration-and-parameters)
     * [Offline usage](#offline-usage)

From 47d55001fad1b74a3603725cdacbc29655a7cb9a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:54:12 +0200
Subject: [PATCH 6/7] Fix YAML validation errors

---
 test-datasets                 |  2 +-
 tools/bowtie2/meta.yml        |  6 +++---
 tools/bwa/index/meta.yml      |  6 +++---
 tools/bwa/mem/meta.yml        | 10 +++++-----
 tools/cutadapt/meta.yml       |  2 +-
 tools/fastq_screen/meta.yml   |  6 +++---
 tools/fastqc/meta.yml         |  7 +++----
 tools/gatk/dict/meta.yml      |  6 +++---
 tools/hisat2/meta.yml         |  6 +++---
 tools/htslib/tabix/meta.yml   |  6 +++---
 tools/multiqc/meta.yml        |  4 ++--
 tools/samtools/faidx/meta.yml |  6 +++---
 tools/samtools/index/meta.yml |  6 +++---
 tools/samtools/sort/meta.yml  |  6 +++---
 tools/shovill/meta.yml        |  2 +-
 tools/tcoffee/meta.yml        |  6 +++---
 tools/trim_galore/meta.yml    |  9 ++++-----
 tools/umi_tools/umi_tools.yml | 10 +++++-----
 18 files changed, 52 insertions(+), 54 deletions(-)

diff --git a/test-datasets b/test-datasets
index aae85a5c..e5fef889 160000
--- a/test-datasets
+++ b/test-datasets
@@ -1 +1 @@
-Subproject commit aae85a5c9c72238959108212481ce83bae569709
+Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b
diff --git a/tools/bowtie2/meta.yml b/tools/bowtie2/meta.yml
index f30ee823..e742b1d0 100644
--- a/tools/bowtie2/meta.yml
+++ b/tools/bowtie2/meta.yml
@@ -28,10 +28,10 @@ output:
         - report:
             type: file
             description: mapping statistics report
-            pattern: *bowtie2_stats.txt
+            pattern: "*bowtie2_stats.txt"
         - alignment:
             type: file
             description: alignment file in BAM format
-            pattern: *bowtie2.bam
+            pattern: "*bowtie2.bam"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"
diff --git a/tools/bwa/index/meta.yml b/tools/bwa/index/meta.yml
index d03c71a2..49fa3c44 100644
--- a/tools/bwa/index/meta.yml
+++ b/tools/bwa/index/meta.yml
@@ -14,12 +14,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - index:
             type: file
             description: bwa indexes file
-            pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+            pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
 authors:
-    - @maxulysse
+    - "@maxulysse"
diff --git a/tools/bwa/mem/meta.yml b/tools/bwa/mem/meta.yml
index 2ea48a28..d8ae9a7d 100644
--- a/tools/bwa/mem/meta.yml
+++ b/tools/bwa/mem/meta.yml
@@ -19,11 +19,11 @@ input:
         - reads:
             type: file
             description: Input fastq file
-            pattern: *.{fastq,fq}
+            pattern: "*.{fastq,fq}"
         - index:
             type: file
             description: bwa indexes file
-            pattern: *.{amb,ann,bwt,pac,sa}
+            pattern: "*.{amb,ann,bwt,pac,sa}"
         - prefix:
             type: val
             description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
@@ -32,11 +32,11 @@ output:
         - bam:
             type: file
             description: Output bam file
-            pattern: *.bam
+            pattern: "*.bam"
         - bamindex:
             type: file
             description: Output bam index file
-            pattern: *.bai
+            pattern: "*.bai"
 
 authors:
-    - @jeremy1805
+    - "@jeremy1805"
diff --git a/tools/cutadapt/meta.yml b/tools/cutadapt/meta.yml
index bb3bb8a8..eee43a07 100644
--- a/tools/cutadapt/meta.yml
+++ b/tools/cutadapt/meta.yml
@@ -33,4 +33,4 @@ output:
             type: file
             description: trimmed FastQ file, or pair of files
 authors:
-    - @piotr-faba-ardigen
+    - "@piotr-faba-ardigen"
diff --git a/tools/fastq_screen/meta.yml b/tools/fastq_screen/meta.yml
index 4b4e56bd..8ec1348e 100644
--- a/tools/fastq_screen/meta.yml
+++ b/tools/fastq_screen/meta.yml
@@ -25,7 +25,7 @@ output:
         - report:
             type: file
             description: FastQ Screen report
-            pattern: *_screen.{txt,html,png}
-            optional_pattern: *_screen.bisulfite_orientation.png
+            pattern: "*_screen.{txt,html,png}"
+            optional_pattern: "*_screen.bisulfite_orientation.png"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"
diff --git a/tools/fastqc/meta.yml b/tools/fastqc/meta.yml
index bfe0f6cf..113ca464 100644
--- a/tools/fastqc/meta.yml
+++ b/tools/fastqc/meta.yml
@@ -27,8 +27,7 @@ output:
         - report:
             type: file
             description: FastQC report
-            pattern: *_fastqc.{zip,html}
+            pattern: "*_fastqc.{zip,html}"
 authors:
-    -
-        - @ewels
-        - @FelixKrueger
+    - "@ewels"
+    - "@FelixKrueger"
diff --git a/tools/gatk/dict/meta.yml b/tools/gatk/dict/meta.yml
index 527d6a69..e03282bb 100644
--- a/tools/gatk/dict/meta.yml
+++ b/tools/gatk/dict/meta.yml
@@ -14,12 +14,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - dict:
             type: file
             description: gatk dictionary file
-            pattern: *.{fasta,fa}.{dict}
+            pattern: "*.{fasta,fa}.{dict}"
 authors:
-    - @maxulysse
+    - "@maxulysse"
diff --git a/tools/hisat2/meta.yml b/tools/hisat2/meta.yml
index d5f5e403..811727a7 100644
--- a/tools/hisat2/meta.yml
+++ b/tools/hisat2/meta.yml
@@ -28,10 +28,10 @@ output:
         - report:
             type: file
             description: mapping statistics report
-            pattern: *hisat2_stats.txt
+            pattern: "*hisat2_stats.txt"
         - alignment:
             type: file
             description: alignment file in BAM format
-            pattern: *hisat2.bam
+            pattern: "*hisat2.bam"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"
diff --git a/tools/htslib/tabix/meta.yml b/tools/htslib/tabix/meta.yml
index d35ec2f2..b8261b92 100644
--- a/tools/htslib/tabix/meta.yml
+++ b/tools/htslib/tabix/meta.yml
@@ -15,12 +15,12 @@ input:
         - input:
             type: file
             description: Input vcf.gz file
-            pattern: *.{vcf.gz}
+            pattern: "*.{vcf.gz}"
 output:
     -
         - index:
             type: file
             description: tabix index file
-            pattern: *.{vcf.gz.tbi}
+            pattern: "*.{vcf.gz.tbi}"
 authors:
-    - @maxulysse
+    - "@maxulysse"
diff --git a/tools/multiqc/meta.yml b/tools/multiqc/meta.yml
index 04e9ca42..86a9799b 100644
--- a/tools/multiqc/meta.yml
+++ b/tools/multiqc/meta.yml
@@ -21,6 +21,6 @@ output:
         - multiqc_report:
             type: file
             description: MultiQC report
-            pattern: *multiqc*.html
+            pattern: "*multiqc*.html"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"
diff --git a/tools/samtools/faidx/meta.yml b/tools/samtools/faidx/meta.yml
index 777eb051..95c2bf4b 100644
--- a/tools/samtools/faidx/meta.yml
+++ b/tools/samtools/faidx/meta.yml
@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - faidx:
             type: file
             description: samtools index fasta file
-            pattern: *.fasta.fai
+            pattern: "*.fasta.fai"
 authors:
-    - @maxulysse
+    - "@maxulysse"
diff --git a/tools/samtools/index/meta.yml b/tools/samtools/index/meta.yml
index e665789b..35d34802 100644
--- a/tools/samtools/index/meta.yml
+++ b/tools/samtools/index/meta.yml
@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 output:
     -
         - index:
             type: file
             description: BAM or CRAM index file
-            pattern: *.{bai}
+            pattern: "*.{bai}"
 authors:
-    - @ewels
+    - "@ewels"
diff --git a/tools/samtools/sort/meta.yml b/tools/samtools/sort/meta.yml
index 60f9e96b..1e042f0d 100644
--- a/tools/samtools/sort/meta.yml
+++ b/tools/samtools/sort/meta.yml
@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 output:
     -
         - sorted_file:
             type: file
             description: Sorted BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 authors:
-    - @ewels
+    - "@ewels"
diff --git a/tools/shovill/meta.yml b/tools/shovill/meta.yml
index 7c204c24..f955fa59 100644
--- a/tools/shovill/meta.yml
+++ b/tools/shovill/meta.yml
@@ -27,4 +27,4 @@ output:
             description: fasta file
             pattern: ${sample_id}.fasta
 authors:
-    - @annacprice
+    - "@annacprice"
diff --git a/tools/tcoffee/meta.yml b/tools/tcoffee/meta.yml
index e15c2e12..1e4a49eb 100644
--- a/tools/tcoffee/meta.yml
+++ b/tools/tcoffee/meta.yml
@@ -16,13 +16,13 @@ input:
         - fasta:
             type: path
             description: Input fasta file
-            pattern: *.{fasta,fa,tfa}
+            pattern: "*.{fasta,fa,tfa}"
 output:
     -
         - alignment:
             type: file
             description: tcoffee alignment file
-            pattern: *.aln
+            pattern: "*.aln"
 
 authors:
-    - @JoseEspinosa
+    - "@JoseEspinosa"
diff --git a/tools/trim_galore/meta.yml b/tools/trim_galore/meta.yml
index b3d42f81..642fb51b 100644
--- a/tools/trim_galore/meta.yml
+++ b/tools/trim_galore/meta.yml
@@ -28,14 +28,13 @@ output:
         - trimmed_fastq:
             type: file
             description: Trimmed FastQ files
-            pattern: *fq.gz
+            pattern: "*fq.gz"
     -
         - report:
             type: file
             description: Trim Galore! trimming report
-            pattern: *trimming_report.txt
+            pattern: "*trimming_report.txt"
 
 authors:
-    -
-        - @ewels
-        - @FelixKrueger
+    - "@ewels"
+    - "@FelixKrueger"
diff --git a/tools/umi_tools/umi_tools.yml b/tools/umi_tools/umi_tools.yml
index b04f0f4e..fcc53b46 100644
--- a/tools/umi_tools/umi_tools.yml
+++ b/tools/umi_tools/umi_tools.yml
@@ -31,15 +31,15 @@ processes:
             - dedupBam:
                 type: tuple
                 description: A tuple of samples id and output bam file
-                pattern: [sample_id, *SAMPLE_ID.dedup.bam]
+                pattern: [sample_id, "*SAMPLE_ID.dedup.bam"]
             - dedupBam:
                 type: tuple
                 description: A tuple of samples id and output bai file
-                pattern: [sample_id, *SAMPLE_ID.dedup.bam.bai]
+                pattern: [sample_id, "*SAMPLE_ID.dedup.bam.bai"]
             - report:
                 type: file
                 description: Log file for the umi_tools operation
-                pattern: *SAMPLE_ID.dedup.log
+                pattern: "*SAMPLE_ID.dedup.log"
 authors:
-    - @candiceh08
-    - @chris-cheshire
+    - "@candiceh08"
+    - "@chris-cheshire"

From 229bd5d0855ac33de1a26ab7e8dfa5cedc9156e9 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:57:17 +0200
Subject: [PATCH 7/7] Update test-datasets

---
 test-datasets | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test-datasets b/test-datasets
index e5fef889..ddbd0c4c 160000
--- a/test-datasets
+++ b/test-datasets
@@ -1 +1 @@
-Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b
+Subproject commit ddbd0c4cf7f1721c78673c4dcc91fcd7940e67f8