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Prempt centrifuge database untar crash

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This commit is contained in:
James A. Fellows Yates 2022-03-26 20:22:35 +00:00
parent 120382f51d
commit 622fafedc8
1 changed files with 4 additions and 1 deletions
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5
subworkflows/local/db_check.nf
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@ -12,6 +12,9 @@ workflow DB_CHECK {
main:
// TODO: make database sheet check
// Checks:
// 1) no duplicates,
// 2) dbs with no special arguments does not have quotes, e.g. just `,,` and NOT `,"",`
parsed_samplesheet = DATABASE_CHECK ( dbsheet )
.csv
.splitCsv ( header:true, sep:',' )
@ -21,7 +24,7 @@ workflow DB_CHECK {
ch_dbs_for_untar = parsed_samplesheet
.branch {
untar: it[1].toString().endsWith(".tar.gz")
untar: it[1].toString().endsWith(".tar.gz") && it[0]['tool'] != 'centrifuge'
skip: true
}