torognes / swarm

A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
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correct example in the man #181

Closed vmikk closed 5 months ago

vmikk commented 5 months ago

I noticed a small inconsistency in the manual regarding the output destination of clusters generated by the swarm command. The manual states, "Clusters are written to the file myfile.swarms", but in the example this data is actually being sent to /dev/null.

This PR updates the swarm command described in the example.

The previous command

zcat myfile.fasta.gz | \
                  swarm \
                      -t 4 \
                      -f \
                      -w myfile.representatives.fasta \
                      -o /dev/null

was updated to

zcat myfile.fasta.gz | \
                  swarm \
                      -t 4 \
                      -f \
                      -w myfile.representatives.fasta \
                      -o myfile.swarms
codecov[bot] commented 5 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (bd9d96a) 98.67% compared to head (df41b27) 98.93%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #181 +/- ## ========================================== + Coverage 98.67% 98.93% +0.26% ========================================== Files 31 31 Lines 3385 3385 ========================================== + Hits 3340 3349 +9 + Misses 45 36 -9 ```

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frederic-mahe commented 5 months ago

Thanks @vmikk !