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Merge pull request #498 from nf-core/dedup-gc-overhead-fix
Dedup gc overhead fix
2 parents d4efd15 + 2f6f473 commit 906b26b

2 files changed

Lines changed: 11 additions & 7 deletions

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conf/base.config

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -95,9 +95,15 @@ process {
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errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' }
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}
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// other process specific exit statuses
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withName: nuclear_contamination {
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errorStrategy = { task.exitStatus in [134] ? 'ignore' : 'retry' }
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}
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withName: multiqc {
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errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
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}
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}
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params {

main.nf

Lines changed: 5 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -584,7 +584,6 @@ if (params.input && (has_extension(params.input, "tsv"))) tsv_path = params.inpu
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ch_input_sample = Channel.empty()
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if (tsv_path) {
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587-
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tsv_file = file(tsv_path)
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if (!tsv_file.exists()) exit 1, "[nf-core/eager] error: input TSV file could not be found. Does the file exist or in the right place? You gave the path: ${params.input}"
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@@ -2608,9 +2607,6 @@ process sex_deterrmine {
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tag "${samplename}"
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publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
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// ANGSD Xcontamination will exit with status 134 when the number of SNPs is too low
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validExitStatus 0,134
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when:
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params.run_nuclear_contamination
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@@ -3057,11 +3053,13 @@ workflow.onComplete {
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log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)"
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} catch (all) {
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// Catch failures and try with plaintext
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def mail_cmd = [ 'mail', '-s', subject, '--content-type=text', email_address ]
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if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
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def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
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if (mqc_report == NULL) {
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log.warn "[nf-core/eager] Could not attach MultiQC report to summary email"
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} else if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
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mail_cmd += [ '-A', mqc_report ]
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}
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mail_cmd.execute() << email_txt
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mail_cmd.execute() << email_html
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log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)"
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}
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}

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