[LINT] move to 4 spaces

bin/src/cutsite_trimming.cpp

@@ -3,11 +3,9 @@
 // Author(s): Nicolas Servant
 // Contact: nicolas.servant@curie.fr
 // This software is distributed without any guarantee under the terms of the BSD-3 licence
-
 // g++ -std=c++0x -o cutsite_trimming cutsite_trimming.cpp
 //./cutsite_trimming -fastq fastq -cutsite AGCTT
 
-
 #include <iostream>     // std::cout
 #include <stdlib.h>
 #include <string.h>
@@ -35,8 +33,8 @@ static int get_options(int argc, char* argv[], std::string& fastqFile,
       if (*opt == '-') {
           if (!strcmp(opt, "--fastq")) {
               fastqFile = std::string(argv[++ac]);
-      } else if (!strcmp(opt, "--cutsite")) {
-
+          }
+	  else if (!strcmp(opt, "--cutsite")) {
 	      std::string cutSitesSequence;
 	      cutSitesSequence = std::string(argv[++ac]);
 	      size_t pos = cutSitesSequence.find(",");
@@ -47,7 +45,6 @@ static int get_options(int argc, char* argv[], std::string& fastqFile,
 		  pos = cutSitesSequence.find(",", begin + 1);
 	      }
 	      cutSites.push_back(cutSitesSequence.substr(begin, pos));
-
 	  } 
 	  else if (!strcmp(opt, "--out")) {
 	      output = std::string(argv[++ac]);
@@ -65,9 +62,7 @@ static int get_options(int argc, char* argv[], std::string& fastqFile,
 
 static int trim_fastq(std::string& fastqFile,
                       std::vector<std::string>& cutSites,
-                      std::string& outFile, bool& rmuntrim)
-{
-
+                      std::string& outFile, bool& rmuntrim){
     int trim_count=0;
     std::string ID;
     std::ifstream ifs (fastqFile);
@@ -125,7 +120,6 @@ static int trim_fastq(std::string& fastqFile,
 
 int main(int argc, char* argv[])
 {
-  
     std::string fastqFile;
     std::vector<std::string> cutSites;
     std::string outFile;

modules/local/trash/bowtie2_end_to_end.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process bowtie2_end_to_end {
-   tag "$sample"
-   label 'process_medium'
-   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_end2end" : params.outdir },
-              saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
-
-   input:
-   tuple val(sample), path(reads)
-   path index
-
-   output:
-   tuple val(sample), path("${prefix}_unmap.fastq"), emit: unmapped_end_to_end
-   tuple val(sample), path("${prefix}.bam"), emit: end_to_end_bam
-
-   script:
-   prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
-   def bwt2_opts = params.bwt2_opts_end2end
-   if (!params.dnase){
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-	${bwt2_opts} \\
-	-p ${task.cpus} \\
-	-x \${INDEX} \\
-	--un ${prefix}_unmap.fastq \\
- 	-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
-   """
-   }else{
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-	${bwt2_opts} \\
-	-p ${task.cpus} \\
-	-x \${INDEX} \\
-	--un ${prefix}_unmap.fastq \\
- 	-U ${reads} > ${prefix}.bam
-   """
-   }
-}

modules/local/trash/bowtie2_on_trimmed_reads.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process bowtie2_on_trimmed_reads {
-   tag "$sample"
-   label 'process_medium'
-   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
-   	      saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
-
-   when:
-   !params.dnase
-
-   input:
-   tuple val(sample), path(reads) 
-   path index 
-
-   output:
-   tuple val(sample), path("${prefix}_trimmed.bam"), emit:trimmed_bam
-
-   script:
-   prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-           ${params.bwt2_opts_trimmed} \\
-           -p ${task.cpus} \\
-           -x \${INDEX} \\
-           -U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
-   """
-}