diff --git a/INSTALL.sh b/INSTALL.sh index 27d1f33..e56aa18 100644 --- a/INSTALL.sh +++ b/INSTALL.sh @@ -7,12 +7,12 @@ bionext_ver="0.3" if [ -d "lib" ]; then { echo "BioNextflow installed" } else { - echo "BioNextflow not installed. Installing it..." - wget https://github.com/biocorecrg/BioNextflow/archive/${bionext_ver}.tar.gz - tar -zvxf ${bionext_ver}.tar.gz - mv "BioNextflow-${bionext_ver}/lib" . - rm ${bionext_ver}.tar.gz - rm -fr BioNextflow-${bionext_ver} + echo "BioNextflow not installed. Installing it..." + wget https://github.com/biocorecrg/BioNextflow/archive/${bionext_ver}.tar.gz + tar -zvxf ${bionext_ver}.tar.gz + mv "BioNextflow-${bionext_ver}/lib" . + rm ${bionext_ver}.tar.gz + rm -fr BioNextflow-${bionext_ver} } fi diff --git a/README.md b/README.md index 60515a9..8642611 100644 --- a/README.md +++ b/README.md @@ -9,24 +9,24 @@ You need to install the library in your nextflow pipeline for being automaticall ### Code before - """ - if [ `echo ${reference_file} | grep ".gz"` ]; then - zcat ${reference_file} > ${index}.fa - bowtie-build --threads ${task.cpus} ${index}.fa ${index} - else - ln -s ${reference_file} ${index}.fa - bowtie-build --threads ${tasks.cpus} ${index}.fa ${index} - fi - """ + """ + if [ `echo ${reference_file} | grep ".gz"` ]; then + zcat ${reference_file} > ${index}.fa + bowtie-build --threads ${task.cpus} ${index}.fa ${index} + else + ln -s ${reference_file} ${index}.fa + bowtie-build --threads ${tasks.cpus} ${index}.fa ${index} + fi + """ ### Code after - def aligner = new NGSaligner(reference_file:genome_file, index:"genome_index", cpus:task.cpus) - aligner.doIndexing("bowtie") + def aligner = new NGSaligner(reference_file:genome_file, index:"genome_index", cpus:task.cpus) + aligner.doIndexing("bowtie") ### Installation Edit the INSTALL.sh file to select the required version - sh INSTALL.sh + sh INSTALL.sh ### Get started