diff --git a/workflow/main.nf b/workflow/main.nf index 36f905d14b95178a30ad9a3488de8c77d95b85ff..1d4104cb6d48bd8df165c800ae63e88c4c7115f4 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -74,6 +74,7 @@ if( ! read ) { error "Didn't match any input files with entries in the design fi // Trim raw reads using trimgalore process trim { + errorStrategy 'ignore' input: set pair_id, file(read1), file(read2) from read @@ -94,6 +95,7 @@ process trim { // Alignment stats with samtools process starfusion { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: @@ -112,6 +114,7 @@ process starfusion { } process align { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: @@ -129,6 +132,7 @@ process align { } process alignqc { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: @@ -184,6 +188,7 @@ process markdups { // Assemble transcripts with stringtie process geneabund { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: @@ -202,6 +207,7 @@ process geneabund { } process statanal { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: @@ -226,6 +232,7 @@ process statanal { } process gatkbam { + errorStrategy 'ignore' publishDir "$params.output", mode: 'copy' input: