Regex expression in nextflow shell

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1

Hi ,

I am running a awk with regex expression in nextflow shell , but it seems not a strightforward things to do in shell , nextflow: this is my code , but it doesnt work :

process POST_proc {
publishDir “${params.output}”, mode: “copy”, overwrite: true

input:
file(f5.vcf)
output:
file(f6.vcf)

shell:
“”"

awk '\$1 !~/#/' f5.vcf | sort -u | awk -F"\t" '{OFS=FS}{for (i=10;i<=NF;i++) if (\$i ~/.\//) \$i='./.'; else \$i=substr(\$i,1,3)}1' >> f6.vcf

"""

}

when i add (awk -F"\t" ‘{OFS=FS}{for (i=10;i<=NF;i++) if ($i ~/.//) $i=’./.‘; else $i=substr($i,1,3)}1’), it doesnt run. seems the regex expression should be changed.

any helps would be appreciated
Regards
Iman

2

Does it run if you double escape the tab separator?

awk -F "\\t"

3

No unfortunately it doesn’t work

4

i could solve it by using templates in shell