How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?

Question

[texaswhiskey1969]

How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?

Here is the code I have tried (not working (it can`t see the input):

parallel './convert2bed --input=vcf < {} > {.}.converted_BED.bed' :::*.vcf

However, it works without GNU parallel:

./convert2bed --input=vcf < SRR5152948_filter.recode.vcf > SRR5152952_converted_BED.bed

Need help how to apply GNU parallel engine correctly.

Thx.

[Alex Reynolds]

You might use the bam2bed_gnuParallel helper script as a basis for something that is tested: https://github.com/bedops/bedops/blob/master/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel

Answer 1

[jean.elbers]

ls *.vcf > samples
parallel './convert2bed --input=vcf < {} > {}.converted_BED.bed' <samples

Note: Not tested with bedops