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typhoidgenomics / genotyphi Public

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Lskatz unittests#28

Open

lskatz wants to merge 21 commits intotyphoidgenomics:maintyphoidgenomics/genotyphi:mainfrom

lskatz:lskatz-unittestslskatz/genotyphi:lskatz-unittestsCopy head branch name to clipboard

Conversation Commits21 (21)Checks Files changed

Open

Lskatz unittests#28
lskatz wants to merge 21 commits intotyphoidgenomics:mainfrom
lskatz:lskatz-unittests

Commits

Commits on Oct 15, 2020

Create unittests.yml
lskatz
authored
Update unittests.yml
lskatz
authored
just v2.7
lskatz
authored
wget single URL via efetch
lskatz
authored
get fastq.gz; run geotyphi step
lskatz
authored
Update unittests.yml
lskatz
authored
fix ct18 fasta file
lskatz
authored
samtools -T
lskatz
authored
Two cpus to reflect two cpus per github runner
lskatz
authored
samtools stdout with -
lskatz
authored
fixed CT18.fasta index name
lskatz
authored
separating out steps with their own names for debugging
lskatz
authored
samtools view -h
lskatz
authored
remove samtools view -
lskatz
authored
samtools fix
lskatz
authored
name of results file
lskatz
authored
Testing on output values
lskatz
authored
speed up apt install with --no-install-recommends
lskatz
authored
fix some spacing in the commenting
lskatz
authored
better debugging statements
lskatz
authored
Update unittests.yml
lskatz
authored

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