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Add option to keep removed contaminants #17

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emnilsson opened this issue Oct 28, 2021 · 0 comments
Open

Add option to keep removed contaminants #17

emnilsson opened this issue Oct 28, 2021 · 0 comments
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enhancement New feature or request
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emnilsson commented Oct 28, 2021

When removing contaminants (e.g. stable RNA) as in #4 we should provide the user with the option of keeping the reads that are filtered out. It is possible to do this with e.g. bbduk by adding outm (outm1 and outm2 for pair-end reads), where matching reads will be stored, see "kmer filtering".

@emnilsson emnilsson added the enhancement New feature or request label Oct 28, 2021
@danilodileo danilodileo self-assigned this Jan 12, 2023
@danilodileo danilodileo added this to the Upgrade v1.1 milestone Jul 5, 2023
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