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Update main.nf to replace 'singularity exec' with 'singularity run' to avoid...

Closed Jonathan Gesell requested to merge patch-1 into master
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@@ -33,7 +33,7 @@ process checkDesignFile {
if (params.astrocyte == true) {
"""
module load singularity/3.0.2;
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-perlcheckdesign-2.0.0.img checkDesignFile.pl --d ${designFile};
singularity run /project/shared/bicf_workflow_ref/singularity_images/bicf-perlcheckdesign-2.0.0.img checkDesignFile.pl --d ${designFile};
"""
} else {
"""
@@ -63,7 +63,7 @@ process downloadSRA {
if (params.astrocyte == true) {
"""
module load singularity/3.0.2;
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-sratoolkit-2.0.0.img bash downloadSRA.sh ${sraNumber} ${sampleID};
singularity run /project/shared/bicf_workflow_ref/singularity_images/bicf-sratoolkit-2.0.0.img bash downloadSRA.sh ${sraNumber} ${sampleID};
"""
} else {
"""
@@ -89,7 +89,7 @@ process rawFastQC {
if (params.astrocyte == true) {
"""
module load singularity/3.0.2;
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-fastqc-2.0.0.img fastqc ${fq} -q -o `pwd -P`;
singularity run /project/shared/bicf_workflow_ref/singularity_images/bicf-fastqc-2.0.0.img fastqc ${fq} -q -o `pwd -P`;
"""
} else {
"""
@@ -112,7 +112,7 @@ process rawMultiQC{
if (params.astrocyte == true) {
"""
module load singularity/3.0.2;
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc -f -n 'SRADownload.MultiQC.Report' ${multiqclist} -o ${output}/QC/Raw;
singularity run /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc -f -n 'SRADownload.MultiQC.Report' ${multiqclist} -o ${output}/QC/Raw;
"""
} else {
"""