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Fix ESMFold crash #222

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Fix ESMFold crash #222

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88a0b84
fix(esmfold): Fixed issue where ESMFold would crash if the basename o…
nbtm-sh Nov 21, 2024
be5635e
feat(changelog): Updated changelog
nbtm-sh Nov 21, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI.
- [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`.
- [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles.
- [[PR #222](https://github.com/nf-core/proteinfold/pull/222)] - Fix issue where ESMFold will crash if sample name does not match it's file name

### Parameters

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5 changes: 3 additions & 2 deletions modules/local/run_esmfold.nf
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Expand Up @@ -14,7 +14,7 @@ process RUN_ESMFOLD {
val numRec

output:
path ("${fasta.baseName}*.pdb"), emit: pdb
path ("*.pdb"), emit: pdb
path ("${fasta.baseName}_plddt_mqc.tsv"), emit: multiqc
path "versions.yml", emit: versions

Expand All @@ -33,7 +33,8 @@ process RUN_ESMFOLD {
--num-recycles ${numRec} \
$args

awk '{print \$2"\\t"\$3"\\t"\$4"\\t"\$6"\\t"\$11}' "${fasta.baseName}"*.pdb | grep -v 'N/A' | uniq > plddt.tsv
SAMPLE_NAME=\$(head -n 1 ${fasta} | cut -d ' ' -f 1 | sed 's/>//')
awk '{print \$2"\\t"\$3"\\t"\$4"\\t"\$6"\\t"\$11}' "\$SAMPLE_NAME"*.pdb | grep -v 'N/A' | uniq > plddt.tsv
echo -e Atom_serial_number"\\t"Atom_name"\\t"Residue_name"\\t"Residue_sequence_number"\\t"pLDDT > header.tsv
cat header.tsv plddt.tsv > "${fasta.baseName}"_plddt_mqc.tsv

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