Expected: When Nextflow reads a CSV file that includes a byte order mark using splitCSV, the byte order mark should be removed. Byte order marks are included in CSV files produced by Excel when saved as a "CSV UTF-8" file.
Actual: Nextflow includes the byte order mark as (invisible) text in the first row.
Steps to reproduce the problem
Save the following CSV text using Excel, in CSV UTF-8 format, as "my_csv.csv":
N E X T F L O W ~ version 21.10.6
Launching bug_test_main.nf [serene_sax] - revision: 281274f014
row contains parameter 'param_1'?: false; row contains parameter 'param_2'?: true
Environment
Nextflow version: 21.10.6
Java version: openjdk 11.0.1 2018-10-16 LTS
Operating system: "CentOS Linux release 7.9.2009 (Core)" (3.10.0-1160.76.1.el7.x86_64)
Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)
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Bug report
Expected behavior and actual behavior
Expected: When Nextflow reads a CSV file that includes a byte order mark using splitCSV, the byte order mark should be removed. Byte order marks are included in CSV files produced by Excel when saved as a "CSV UTF-8" file.
Actual: Nextflow includes the byte order mark as (invisible) text in the first row.
Steps to reproduce the problem
Save the following CSV text using Excel, in CSV UTF-8 format, as "my_csv.csv":
param_1,param_2 val_1,val_2
Nextflow file:
Expected output: "row contains parameter 'param_1'?: true; row contains parameter 'param_2'?: true"
Actual output: "row contains parameter 'param_1'?: false; row contains parameter 'param_2'?: true"
Program output
N E X T F L O W ~ version 21.10.6 Launching
bug_test_main.nf
[serene_sax] - revision: 281274f014 row contains parameter 'param_1'?: false; row contains parameter 'param_2'?: trueEnvironment
Additional context
nextflow.log