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Snpsites (#480)

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* output constant sites as a val as well as a file so it can be passed into iqtree

* Using an env variable because that's far safer!

* Update software/snpsites/main.nf

* remove hardcoded param that should be a user option

* Update software/snpsites/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Anthony Underwood 2021-05-06 16:05:07 +01:00 committed by GitHub
parent b6e4ecabba
commit 4422454ba5
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2 changed files with 3 additions and 2 deletions
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3
software/snpsites/main.nf
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@ -29,8 +29,9 @@ process SNPSITES {
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
""" """
snp-sites -c \\ snp-sites \\
$alignment \\ $alignment \\
$options.args \\
> filtered_alignment.fas > filtered_alignment.fas
echo \$(snp-sites -C $alignment) > constant.sites.txt echo \$(snp-sites -C $alignment) > constant.sites.txt

2
tests/software/snpsites/test.yml
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@ -4,6 +4,6 @@
- snpsites - snpsites
files: files:
- path: output/snpsites/filtered_alignment.fas - path: output/snpsites/filtered_alignment.fas
md5sum: 34a3d2ae4439447eabe80282f4625dba md5sum: f96c7513003e878e16fa9eac9fcda0f4
- path: output/snpsites/constant.sites.txt - path: output/snpsites/constant.sites.txt
md5sum: 8b9b226e3787f7baaefce07405af22c9 md5sum: 8b9b226e3787f7baaefce07405af22c9