Fix editor config styles

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "test-datasets"]
-	path = test-datasets
+    path = test-datasets
-	url = https://github.com/nf-core/test-datasets.git
+    url = https://github.com/nf-core/test-datasets.git

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
 

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.
+    // 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
+    // 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)
+        tuple val(name), path(reads)
-		val (outdir)
+        val (outdir)
-		val (bowtie2_args)
+        val (bowtie2_args)
-		val (verbose)
+        val (verbose)
 
-	output:
+    output:
-	    path "*bam",  emit: bam
+        path "*bam",  emit: bam
-		path "*stats.txt", emit: stats 
+        path "*stats.txt", emit: stats
 
-	publishDir "$outdir/bowtie2",
+    publishDir "$outdir/bowtie2",
-		mode: "copy", overwrite: true
+        mode: "copy", overwrite: true
 
-	script:
+    script:
-		if (verbose){
+        if (verbose){
-			println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
+            println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
-		}
+        }
 
-		cores = 4
+        cores = 4
 
-		readString = ""
+        readString = ""
 
-		// Options we add are
+        // Options we add are
-		bowtie2_options = bowtie2_args
+        bowtie2_options = bowtie2_args
-		bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
+        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"]
 
-		"""
+        // single-end / paired-end distinction. Might also be handled via params.single_end
-		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
+        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
+        """
 
 }

tools/bowtie2/meta.yml

@@ -1,4 +1,4 @@
-name: Bowtie 2 
+name: Bowtie 2
 description: Ultrafast alignment to reference genome
 keywords:
     - Alignment

tools/bwa/index/main.nf

@@ -13,4 +13,4 @@ process bwa_index {
     """
     bwa index ${fasta}
     """
-}
+}

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
-
-

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} \
+                        -j ${task.cpus} \
-		            	-q $params.cutadapt_min_quality \
+                        -q $params.cutadapt_min_quality \
-		            	--minimum-length $params.cutadapt_min_length \
+                        --minimum-length $params.cutadapt_min_length \
-		            	--output ${forward_fq} \
+                        --output ${forward_fq} \
-		            	${reads}
+                        ${reads}
                     """
     } else {
         processing = """
                     cutadapt \
-		            	-j ${task.cpus} \
+                        -j ${task.cpus} \
-		            	-q $params.cutadapt_min_quality \
+                        -q $params.cutadapt_min_quality \
-		            	--minimum-length $params.cutadapt_min_length \
+                        --minimum-length $params.cutadapt_min_length \
-		            	--pair-filter=any \
+                        --pair-filter=any \
-		            	--output ${forward_fq} \
+                        --output ${forward_fq} \
-		            	--paired-output ${reverse_fq} ${reads}
+                        --paired-output ${reverse_fq} ${reads}
-            
+
-                    
+
                     """
     }
 

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 
+            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 
+            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/

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!
+    // depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
-	// label 'bigMem'
+    // label 'bigMem'
-	// label 'multiCore'
+    // label 'multiCore'
 
     input:
-	    tuple val(name), path(reads)
+        tuple val(name), path(reads)
-		val (outputdir)
+        val (outputdir)
-		// fastq_screen_args are best passed in to the workflow in the following manner:
+        // fastq_screen_args are best passed in to the workflow in the following manner:
-		// --fastq_screen_args="--subset 200000 --force"
+        // --fastq_screen_args="--subset 200000 --force"
-		val (fastq_screen_args)  
+        val (fastq_screen_args)
-		val (verbose)
+        val (verbose)
 
-	output:
+    output:
-	    path "*png",  emit: png
+        path "*png",  emit: png
-	    path "*html", emit: html
+        path "*html", emit: html
-		path "*txt",  emit: report
+        path "*txt",  emit: report
 
-	publishDir "$outputdir",
+    publishDir "$outputdir",
-		mode: "link", overwrite: true
+        mode: "link", overwrite: true
 
     script:
-		println(name)
+        println(name)
-		println(reads)
+        println(reads)
-		println(outputdir)
+        println(outputdir)
-		if (verbose){
+        if (verbose){
-			println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
+            println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
-		}
+        }
 
-	"""
+    """
-	module load fastq_screen
+    module load fastq_screen
-	fastq_screen $fastq_screen_args $reads
+    fastq_screen $fastq_screen_args $reads
-	"""
+    """
 
-}
+}

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 /

tools/fastqc/main.nf

@@ -1,37 +1,37 @@
 nextflow.preview.dsl = 2
 
-process FASTQC {	
+process FASTQC {
-    
+
     // tag "FastQC - $sample_id"
 
-	input:
+    input:
-	    tuple val(name), path(reads)
+        tuple val(name), path(reads)
-		val (outputdir)
+        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 (fastqc_args)
-		val (verbose)
+        val (verbose)
 
-	output:
+    output:
-	    tuple val(name), path ("*fastqc*"), emit: all
+        tuple val(name), path ("*fastqc*"), emit: all
-		path "*.zip",                       emit: report // e.g. for MultiQC later
+        path "*.zip",                       emit: report // e.g. for MultiQC later
-	
-    // container 'quay.io/biocontainers/fastqc:0.11.8--2' 
 
-	publishDir "$outputdir",
+    // container 'quay.io/biocontainers/fastqc:0.11.8--2'
-		mode: "copy", overwrite: true
 
-	script:
+    publishDir "$outputdir",
+        mode: "copy", overwrite: true
 
-		if (verbose){
+    script:
-			println ("[MODULE] FASTQC ARGS: " + fastqc_args)
-		}
 
-		"""
+        if (verbose){
-		module load fastqc
+            println ("[MODULE] FASTQC ARGS: " + fastqc_args)
-		fastqc $fastqc_args -q -t 2 $reads
+        }
+
+        """
+        module load fastqc
+        fastqc $fastqc_args -q -t 2 $reads
 
         fastqc --version &> fastqc.version.txt
-		"""
+        """
 
 }

tools/fastqc/meta.yml

@@ -29,6 +29,6 @@ output:
             description: FastQC report
             pattern: *_fastqc.{zip,html}
 authors:
-    - 
+    -
         - @ewels
         - @FelixKrueger

tools/gatk/dict/main.nf

@@ -16,4 +16,4 @@ process gatk_dict {
         --REFERENCE ${fasta} \
         --OUTPUT ${fasta.baseName}.dict
     """
-}
+}

tools/gatk/dict/meta.yml

@@ -22,4 +22,4 @@ output:
             description: gatk dictionary file
             pattern: *.{fasta,fa}.{dict}
 authors:
-    - @maxulysse
+    - @maxulysse

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"]

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

tools/htslib/tabix/meta.yml

@@ -23,4 +23,4 @@ output:
             description: tabix index file
             pattern: *.{vcf.gz.tbi}
 authors:
-    - @maxulysse
+    - @maxulysse

tools/multiqc/main.nf

@@ -1,31 +1,31 @@
 nextflow.preview.dsl=2
 
 process MULTIQC {
-	
+
     // tag "FastQC - $sample_id"
-    
+
     input:
-	    path (file)
+        path (file)
-		val (outdir)
+        val (outdir)
-		val (multiqc_args)
+        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:
+    output:
-	    path "*html",       emit: html
+        path "*html",       emit: html
 
-	publishDir "${outdir}/multiqc",
+    publishDir "${outdir}/multiqc",
-		mode: "copy", overwrite: true
+        mode: "copy", overwrite: true
 
     script:
 
-		if (verbose){
+        if (verbose){
-			println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
+            println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
-		}
+        }
 
-		"""
+        """
-		multiqc $multiqc_args -x work . 
+        multiqc $multiqc_args -x work .
-		"""
+        """
 
 }

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 /

tools/samtools/faidx/meta.yml

@@ -24,4 +24,4 @@ output:
             description: samtools index fasta file
             pattern: *.fasta.fai
 authors:
-    - @maxulysse
+    - @maxulysse

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

tools/tcoffee/main.nf

@@ -14,4 +14,3 @@ process tcoffee {
     t_coffee -seq $fasta -outfile ${fasta}.aln
     """
 }
-

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 /

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:
+    input:
-	    tuple val (name), path (reads)
+        tuple val (name), path (reads)
-		val (outdir)
+        val (outdir)
-		val (trim_galore_args)
+        val (trim_galore_args)
-		val (verbose)
+        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 "${outdir}/trim_galore",
+    publishDir "${outdir}/trim_galore",
-		mode: "copy", overwrite: true
+        mode: "copy", overwrite: true
 
     script:
-		if (verbose){
+        if (verbose){
-			println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
+            println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
-		}
+        }
-		
+
         trim_galore_args += " --gzip "           // we like small files
 
-		pairedString = 0
+        pairedString = 0
-		if (reads instanceof List) {
+        if (reads instanceof List) {
-			pairedString = 1
+            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
+        module load trim_galore
-		trim_galore $trim_galore_args $reads
+        trim_galore $trim_galore_args $reads
-		"""
+        """
 
 }
 
 
 
- 
 
 
-  
+
 

tools/trim_galore/meta.yml

@@ -36,6 +36,6 @@ output:
             pattern: *trimming_report.txt
 
 authors:
-    - 
+    -
         - @ewels
         - @FelixKrueger

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:$PATH
+ENV PATH /opt/conda/envs/nfcore-module-umitools/bin:$PATH

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

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
-