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

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 'bigMem'
-	// label 'multiCore'
+    // 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 
+        // single-end / paired-end distinction. Might also be handled via params.single_end
-		if (reads instanceof List) {
+        if (reads instanceof List) {
-			readString = "-1 " + reads[0] + " -2 " + reads[1]
+            readString = "-1 " + reads[0] + " -2 " + reads[1]
-		}
+        }
-		else {
+        else {
-			readString = "-U " + reads
+            readString = "-U " + reads
-		}
+        }
 
-		index = params.genome["bowtie2"]
+        index = params.genome["bowtie2"]
-		bowtie2_name = name + "_" + params.genome["name"]
+        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
+        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/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

@@ -17,21 +17,21 @@ process cutadapt {
     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/fastq_screen/main.nf

@@ -2,37 +2,37 @@ 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

@@ -4,34 +4,34 @@ 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 "$outputdir",
+    publishDir "$outputdir",
-		mode: "copy", overwrite: true
+        mode: "copy", overwrite: true
 
-	script:
+    script:
 
-		if (verbose){
+        if (verbose){
-			println ("[MODULE] FASTQC ARGS: " + fastqc_args)
+            println ("[MODULE] FASTQC ARGS: " + fastqc_args)
-		}
+        }
 
-		"""
+        """
-		module load fastqc
+        module load fastqc
-		fastqc $fastqc_args -q -t 2 $reads
+        fastqc $fastqc_args -q -t 2 $reads
 
         fastqc --version &> fastqc.version.txt
-		"""
+        """
 
 }

tools/multiqc/main.nf

@@ -5,27 +5,27 @@ 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/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

@@ -18,15 +18,15 @@ 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:
+    output:
-	    tuple val(name), path ("*fq.gz"),             emit: reads
+        tuple val(name), path ("*fq.gz"),             emit: reads
-		path "*trimming_report.txt", optional: true,  emit: report
+        path "*trimming_report.txt", optional: true,  emit: report
 
         // Trimming reports are not generated for e.g. --hardtrim5, --clock etc
         // saveAs: {filename ->
@@ -34,21 +34,21 @@ process TRIM_GALORE {
         //   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} "
@@ -85,10 +85,10 @@ process TRIM_GALORE {
             }
         }
 
-		"""
+        """
-		module load trim_galore
+        module load trim_galore
-		trim_galore $trim_galore_args $reads
+        trim_galore $trim_galore_args $reads
-		"""
+        """
 
 }
 
@@ -98,4 +98,3 @@ process TRIM_GALORE {
 
 
 
-

tools/umi_tools/Dockerfile

@@ -1,6 +1,6 @@
 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 /

tools/umi_tools/umi_tools.yml

@@ -43,4 +43,3 @@ processes:
 authors:
     - @candiceh08
     - @chris-cheshire
-