Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
66 lines
1.8 KiB
Plaintext
66 lines
1.8 KiB
Plaintext
nextflow.enable.dsl=2
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process VCF2PROT {
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memory 2.GB
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container "${params.container_vcf2prot}"
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containerOptions "${params.containerOptions}"
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// echo true
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publishDir "${params.outdir}/vcf2prot", mode: 'copy'
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stageInMode 'copy'
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maxForks 1
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input:
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path vcf
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path vcf_filtered
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output:
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path "*.fasta"
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script:
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"""
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#!/bin/bash
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workdir=`pwd`
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patient_name=\$(basename $vcf .vcf)
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grep '^#' $vcf > work1.vcf
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/opt/conda/envs/vcf2prot/bin/python3 -c "
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import pickle
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import numpy as np
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import pandas as pd
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with open('$vcf_filtered', 'rb') as fp:
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vcf_file = pickle.load(fp)
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vcf_filtered=[]
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for i in vcf_file:
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vcf_filtered.extend(i[1])
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vcf_filtered = pd.DataFrame(vcf_filtered)
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#drop duplicates, it returns error, consequence of overlapping genes on genome
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vcf_filtered = vcf_filtered.drop_duplicates()
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vcf_filtered = vcf_filtered.replace({'chr':''}, regex=True)
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vcf_filtered = vcf_filtered.sort_values(by=[0,1])
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with open('work1.vcf', 'a') as f:
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for line in np.array(vcf_filtered):
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li = str(line).replace('[', '').replace(']', '').replace('\\'', '').replace(' ', '\\t').replace('\\n', '')
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f.write(f'{li}\\n')
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"
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awk '{gsub(/^##contig=<ID=chr/,"##contig=<ID="); print}' work1.vcf > \$workdir/work_2.vcf
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###remove non canonical chromososms
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grep -v '[0-9]_\\|Y_\\|X_\\|Un_' \$workdir/work_2.vcf > \$workdir/work.vcf
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###
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bcftools csq -f /home/omic/Homo_sapiens.GRCh38.dna.toplevel.fa -g /home/omic/Homo_sapiens.GRCh38.112.gff3 \$workdir/work.vcf --phase a --ncsq 120 -O v -o \$workdir/annotated.vcf
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/home/omic/vcf2prot/bins/Linux/vcf2prot -f \$workdir/annotated.vcf -r /home/omic/vcf2prot/MANE_transcipts_reference.fasta -v -g st -o \$workdir
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mv *.fasta \${patient_name}_transcript_id_mutations.fasta
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"""
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}
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