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support for alignment #52

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Nov 2, 2023
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support for alignment
Henning Onsbring committed Nov 2, 2023
commit 87d0d44a2c6394b6374839430345f99d4a885ba7
7 changes: 7 additions & 0 deletions modules/spaceranger/main.nf
Original file line number Diff line number Diff line change
@@ -43,6 +43,12 @@ process SPACECOUNT {
else {
image_argument = ""
}
if ( alignment != "n") {
alignment_argument = "--loupe-alignment="+params.outdir+'/'+Sample_Project+'/metadata/'+alignment
}
else {
alignment_argument = ""
}


"""
@@ -58,6 +64,7 @@ process SPACECOUNT {
$dark_argument \
$cyta_argument \
$probe_argument \
$alignment_argument \
"""
stub:
"""