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Fix clusterOptions syntax #509

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Fix clusterOptions syntax #509

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21 changes: 7 additions & 14 deletions pipelines/annotation_pipeline.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,7 @@ workflow {
* to genes and functional consequences.
*/
process runSnpIndel {
clusterOptions "-o ${batchRoot}/logs/consequence_snp.out \
-e ${batchRoot}/logs/consequence_snp.err"
clusterOptions "-o ${batchRoot}/logs/consequence_snp.out", "-e ${batchRoot}/logs/consequence_snp.err"

publishDir "${batchRoot}/gene_mapping",
overwrite: true,
Expand Down Expand Up @@ -135,8 +134,7 @@ process runSnpIndel {
* Extract repeat expansion variants from ClinVar and map them to genes.
*/
process runRepeat {
clusterOptions "-o ${batchRoot}/logs/consequence_repeat.out \
-e ${batchRoot}/logs/consequence_repeat.err"
clusterOptions "-o ${batchRoot}/logs/consequence_repeat.out", "-e ${batchRoot}/logs/consequence_repeat.err"

publishDir "${batchRoot}/gene_mapping",
overwrite: true,
Expand Down Expand Up @@ -166,8 +164,7 @@ process runRepeat {
* known repeat expansions).
*/
process runStructural {
clusterOptions "-o ${batchRoot}/logs/consequence_structural.out \
-e ${batchRoot}/logs/consequence_structural.err"
clusterOptions "-o ${batchRoot}/logs/consequence_structural.out", "-e ${batchRoot}/logs/consequence_structural.err"

publishDir "${batchRoot}/gene_mapping",
overwrite: true,
Expand Down Expand Up @@ -268,8 +265,7 @@ process checkLatestMappings {
* Generate annotated ClinVar XML
*/
process generateAnnotatedXml {
clusterOptions "-o ${batchRoot}/logs/annotated_xml_generation.out \
-e ${batchRoot}/logs/annotated_xml_generation.err"
clusterOptions "-o ${batchRoot}/logs/annotated_xml_generation.out", "-e ${batchRoot}/logs/annotated_xml_generation.err"

publishDir "${batchRoot}",
overwrite: true,
Expand Down Expand Up @@ -322,8 +318,7 @@ process countClinvarRecords {
* Generate the evidence strings for submission to Open Targets.
*/
process generateEvidence {
clusterOptions "-o ${batchRoot}/logs/evidence_string_generation_${startEnd[0]}.out \
-e ${batchRoot}/logs/evidence_string_generation_${startEnd[0]}.err"
clusterOptions "-o ${batchRoot}/logs/evidence_string_generation_${startEnd[0]}.out", "-e ${batchRoot}/logs/evidence_string_generation_${startEnd[0]}.err"

// Removed mappings are the same for each process, so no need to aggregate
publishDir "${batchRoot}/logs",
Expand Down Expand Up @@ -410,8 +405,7 @@ process collectInvalidEvidence {
process collectCounts {
label 'short_time'
label 'small_mem'
clusterOptions "-o ${batchRoot}/logs/collect_counts.out \
-e ${batchRoot}/logs/collect_counts.err"
clusterOptions "-o ${batchRoot}/logs/collect_counts.out", "-e ${batchRoot}/logs/collect_counts.err"

publishDir "${batchRoot}/logs",
overwrite: true,
Expand Down Expand Up @@ -453,8 +447,7 @@ process checkDuplicates {
* Convert MedGen and OMIM cross-references into ZOOMA format.
*/
process convertXrefs {
clusterOptions "-o ${batchRoot}/logs/traits_to_zooma_format.out \
-e ${batchRoot}/logs/traits_to_zooma_format.err"
clusterOptions "-o ${batchRoot}/logs/traits_to_zooma_format.out", "-e ${batchRoot}/logs/traits_to_zooma_format.err"

publishDir "${batchRoot}/clinvar",
overwrite: true,
Expand Down
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