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The pipeline creates 2 hifiasm output files #136

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MartinPippel opened this issue Nov 8, 2024 · 0 comments
Open

The pipeline creates 2 hifiasm output files #136

MartinPippel opened this issue Nov 8, 2024 · 0 comments

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@MartinPippel
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Describe the bug
The pipeline creates two assembly files in the corresponding output directory 03_assembly/hifiasm-raw-default:

-rw-r--r-- 1 pippel pg_snic2021-6-194  101M Nov  1 17:45 hifiasm-raw-default.asm.bp.p_ctg.fasta.gz
-rw-r--r-- 1 pippel pg_snic2021-6-194   92M Nov  1 17:46 hifiasm-raw-default.asm.bp.p_ctg.fasta.fasta.gz

Which is not necessary they contain the same information one is folded and the other one has the full contig sequnce on one line.
We just need the folded one.

To Reproduce
Steps to reproduce the behavior:
Run the ASSEMBLE_HIFI subworkflow in default mode.

Expected behavior
Only one file should be published.

Solution
Just publish the fasta file from the GFATOOLS_GFA2FA process and exclude it from the HIFIASM process.

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