- 23 Aug, 2021 12 commits
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Cecilia-Sensalari authored
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lohausr authored
* Condense, improve and clean up Nextflow logging - tries to remedy visual issues in ANSI console by condensing and shortening line lengths of log output - improves some wording, consistency and whitespacing of log output - refactor some log output code into functions - adds ksrates version to log * Don't clean up if ksrates config file newly generated There won't be anything to clean up, and onComplete would print irrelevant warning about empty focal_species parameter. * Single '/' in logs folder path when focal_species empty * Some renaming of channels and variables - Correction -> Adjustment - peakCalling -> paralogsAnalyses
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Cecilia-Sensalari authored
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Rolf Lohaus authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
- If log file exists and ERROR lines exist, point only to the log file and not to the error report above.
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
- Added error message when logfile exists but there are no ERROR lines - Reduce code redundacy
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Cecilia Sensalari authored
* LMM warns and skips if components > datapoints
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Cecilia-Sensalari authored
- Print messages from errorReport and errorMessage also in case of existing log file with no ERROR lines in it to provide more guidance. - The structure of the error handling is the same but with less redundancy (printing the headline is now done only once; "Caused by" line is done only once)
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- 22 Aug, 2021 7 commits
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia Sensalari authored
* When pipeline crashes, an error box is shown at the end of Nextflow error report: it prints the name of the stopped process, the error lines (if available) and points to the concerned log file(s) for more details. * Update FAQs with error box description and figures
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Cecilia Sensalari authored
Co-authored-by:
lohausr <56632794+lohausr@users.noreply.github.com>
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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- 20 Aug, 2021 18 commits
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https://github.com/VIB-PSB/ksratesCecilia-Sensalari authored
Merge branch 'nextflow_error_report' of https://github.com/VIB-PSB/ksrates into nextflow_error_report
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Cecilia-Sensalari authored
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Cecilia Sensalari authored
Co-authored-by:
lohausr <56632794+lohausr@users.noreply.github.com>
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
- If errorReport gives nothing useful, apply the same to errorMessage - If species names are still unknown, point to a generic wgd_ortholog_
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia Sensalari authored
Co-authored-by:
lohausr <56632794+lohausr@users.noreply.github.com>
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Cecilia-Sensalari authored
- both in onComplete and onError - onComplete will print that it can't delete possible leftovers in paralog_distrib. - onError will prints a message pointing to the log file without using the whole path
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
- both in onError and onComplete
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https://github.com/VIB-PSB/ksratesCecilia-Sensalari authored
Merge branch 'nextflow_error_report' of https://github.com/VIB-PSB/ksrates into nextflow_error_report
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Cecilia-Sensalari authored
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Cecilia Sensalari authored
Co-authored-by:
lohausr <56632794+lohausr@users.noreply.github.com>
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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- 19 Aug, 2021 3 commits
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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Cecilia-Sensalari authored
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