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Dedup gc overhead fix #498

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Merged
jfy133 merged 10 commits into from
Jul 13, 2020
Merged

Dedup gc overhead fix #498

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4946b93
Remove deprecated validExitStatus code
jfy133 Jun 30, 2020
9d862c6
HTML reports instead of text for mail
jfy133 Jun 30, 2020
dc14190
Replace file with path EVERYWHERE
jfy133 Jun 30, 2020
178ae43
Roll back some of the file>path
jfy133 Jun 30, 2020
25dc17e
Revert "Roll back some of the file>path"
jfy133 Jun 30, 2020
5a2f3e7
Revert "Replace file with path EVERYWHERE"
jfy133 Jun 30, 2020
7c7e878
remove TODO
jfy133 Jun 30, 2020
33143b0
Fix emailing on crash
jfy133 Jul 1, 2020
c823cd1
Remove left overattempts from file>path
jfy133 Jul 1, 2020
2f6f473
Merge branch 'dev' into dedup-gc-overhead-fix
jfy133 Jul 12, 2020
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6 changes: 6 additions & 0 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -95,9 +95,15 @@ process {
errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' }
}

// other process specific exit statuses
withName: nuclear_contamination {
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errorStrategy = { task.exitStatus in [134] ? 'ignore' : 'retry' }
}

withName: multiqc {
errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
}

}

params {
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12 changes: 5 additions & 7 deletions main.nf
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Expand Up @@ -584,7 +584,6 @@ if (params.input && (has_extension(params.input, "tsv"))) tsv_path = params.inpu
ch_input_sample = Channel.empty()
if (tsv_path) {


tsv_file = file(tsv_path)
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}"

Expand Down Expand Up @@ -2609,9 +2608,6 @@ process sex_deterrmine {
tag "${samplename}"
publishDir "${params.outdir}/nuclear_contamination", mode:"copy"

// ANGSD Xcontamination will exit with status 134 when the number of SNPs is too low
validExitStatus 0,134

when:
params.run_nuclear_contamination

Expand Down Expand Up @@ -3058,11 +3054,13 @@ workflow.onComplete {
log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)"
} catch (all) {
// Catch failures and try with plaintext
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text', email_address ]
if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
if (mqc_report == NULL) {
log.warn "[nf-core/eager] Could not attach MultiQC report to summary email"
} else if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_txt
mail_cmd.execute() << email_html
log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)"
}
}
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