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Optional filtering of the alignments input to last/dotplot. #7429

Merged
merged 1 commit into from
Feb 4, 2025
Merged

Optional filtering of the alignments input to last/dotplot. #7429

merged 1 commit into from
Feb 4, 2025

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charles-plessy
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@charles-plessy charles-plessy commented Feb 4, 2025 •
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This uses the maf-filter tool distributed together with last-dotplot in the LAST suite.

The genome alignments that are plotted can be very large, even after the filtering step. Therefore I implemented it with a pipe command rather than creating a separate module, which would consume a lot of disk space.

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@charles-plessy
Optional filtering of the alignments input to last/dotplot.
ae242ae 
This uses the `maf-filter` tool distributed together with `last-dotplot`
in the LAST suite.

The genome alignments that are plotted can be very large, even after the
filtering step.  Therefore I implemented it with a pipe command rather
than creating a separate module, which would consume a lot of disk
space.
kubranarci
kubranarci approved these changes Feb 4, 2025
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LGTM!

modules/nf-core/last/dotplot/main.nf
@@ -22,18 +23,21 @@ process LAST_DOTPLOT {

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
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why not to take all args in one? is there a specific reason?

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okay saw it now :D

@charles-plessy charles-plessy added this pull request to the merge queue Feb 4, 2025
Merged via the queue into master with commit 83fb0b4 Feb 4, 2025
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@charles-plessy charles-plessy deleted the last_dotplot_filtered branch February 4, 2025 10:02
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@kubranarci kubranarci kubranarci approved these changes

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