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Fix csv splitter when skipping empty lines #6586

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Merged
bentsherman merged 1 commit into from
Nov 19, 2025
Merged

Fix csv splitter when skipping empty lines #6586

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2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/splitter/CsvSplitter.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ class CsvSplitter extends AbstractTextSplitter {
String line
int z = 0

while( z++ < skipLines && reader.readLine()) { /* nope */ }
while( z++ < skipLines && reader.readLine() != null ) { /* nope */ }

if( firstLineAsHeader ) {
line = reader.readLine()
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16 changes: 16 additions & 0 deletions modules/nextflow/src/test/groovy/nextflow/splitter/CsvSplitterTest.groovy
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Expand Up @@ -90,6 +90,22 @@ class CsvSplitterTest extends Specification {
items[0] == ['gamma', '', 'zeta']
items[1] == ['eta', 'theta', 'iota']
items[2] == ['mu', 'nu', 'xi']

when:
def LINES = '''
alpha,beta,delta

gamma,,zeta
eta,theta,iota
pi,rho,sigma
'''
.stripIndent().trim()
items = new CsvSplitter().target(LINES).options(skip:3).list()
then:
items.size() == 2
items[0] instanceof List
items[0] == ['eta', 'theta', 'iota']
items[1] == ['pi', 'rho', 'sigma']
}

def testSplitWithCount() {
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