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ignore artic-medaka fails with exit status 20 #288

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2 changes: 1 addition & 1 deletion poreCov.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -313,7 +313,7 @@ workflow {

// rename barcodes based on --samples input.csv
if (params.samples) { fastq_input_ch = fastq_input_raw_ch.join(samples_input_ch).map { it -> tuple(it[2],it[1])}
fastq_input_raw_ch.join(samples_input_ch).ifEmpty{ exit 2, "Could not match barcode numbers from $params.samples to the read files, some typo?"}
fastq_input_raw_ch.join(samples_input_ch).ifEmpty{ exit 2, "Could not match barcode numbers from $params.samples to the read files, some typo?"}
}
else if (!params.samples) { fastq_input_ch = fastq_input_raw_ch }

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2 changes: 2 additions & 0 deletions workflows/process/artic.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
process artic_medaka {
label 'artic'
errorStrategy {task.exitStatus == 20 ? 'ignore' : 'retry'}
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
Expand Down Expand Up @@ -68,6 +69,7 @@ process artic_medaka {

process artic_medaka_custom_bed {
label 'artic'
errorStrategy {task.exitStatus == 20 ? 'ignore' : 'retry'}
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
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