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remove BUSCO warning from stdout log #402

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Lumimar opened this issue Mar 3, 2023 · 1 comment · Fixed by #442
Closed

remove BUSCO warning from stdout log #402

Lumimar opened this issue Mar 3, 2023 · 1 comment · Fixed by #442
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enhancement New feature or request

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@Lumimar
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Lumimar commented Mar 3, 2023

Description of feature

at the moment BUSCO's no gene warning is reported in the STDOUT log where pipeline errors are normally highlighted, but given that it is expected that this might happen in some cases it might be better to remove the warning. Currently the warning is displayed like this (lines 3-7) at the end of the run:

[c6/eb468a] process > NFCORE_MAG:mag:CUSTOM_DUMPS... [100%] 1 of 1 ✔
[c3/8aa445] process > NFCORE_MAG:mag:MULTIQC         [100%] 1 of 1 ✔
-[nf-core/mag] For 2 bin(s) BUSCO did not find any matching genes:
    SPAdes-MaxBin2-test_minigut_sample2.noclass.2.fa
    SPAdes-MaxBin2-test_minigut_sample2.noclass.1.fa
See /home/lmarcell/out/GenomeBinning/QC/BUSCO/[bin]_busco.log for further information.-
-[nf-core/mag] Pipeline completed successfully, but with errored process(es) -
Completed at: 03-Mar-2023 11:34:55
Duration    : 34m 39s
CPU hours   : 1.0 (0.1% failed)
Succeeded   : 150
Ignored     : 1
Failed      : 1

Many thanks!
Lucio

@Lumimar Lumimar added the enhancement New feature or request label Mar 3, 2023
@jfy133 jfy133 self-assigned this Mar 23, 2023
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jfy133 commented May 11, 2023

@jfy133 jfy133 linked a pull request May 11, 2023 that will close this issue
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@jfy133 jfy133 closed this as completed May 11, 2023
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