splitCsv includes the byte order mark as part of the first column of the first line.

[sclamons]

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:

nextflow.enable.dsl = 2

workflow {
  Channel.fromPath('my_csv.csv') | splitCsv(header:true, strip:true) | view {"row contains parameter 'param_1'?: ${it.containsKey('param_1')}; row contains parameter 'param_2'?: ${it.containsKey('param_2')}"}
}

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'?: 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)

Additional context

nextflow.log

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.