Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

main_vcf2prot.nf

@@ -0,0 +1,65 @@
+nextflow.enable.dsl=2
+
+process VCF2PROT {
+  memory 2.GB
+
+  container "${params.container_vcf2prot}"
+  containerOptions "${params.containerOptions}"
+  // echo true
+  publishDir "${params.outdir}/vcf2prot", mode: 'copy'
+  stageInMode 'copy'
+  maxForks 1
+
+  input:
+    path vcf
+    path vcf_filtered
+
+  output:
+    path "*.fasta"
+
+  script:
+    """
+    #!/bin/bash
+    workdir=`pwd`
+    patient_name=\$(basename $vcf .vcf)
+
+    grep '^#' $vcf > work1.vcf
+
+    /opt/conda/envs/vcf2prot/bin/python3 -c "
+import pickle
+import numpy as np
+import pandas as pd
+
+with open('$vcf_filtered', 'rb') as fp:
+    vcf_file = pickle.load(fp)
+    
+vcf_filtered=[]
+for i in vcf_file:
+    vcf_filtered.extend(i[1])
+    
+vcf_filtered = pd.DataFrame(vcf_filtered)
+
+#drop duplicates, it returns error, consequence of overlapping genes on genome
+vcf_filtered = vcf_filtered.drop_duplicates()
+
+vcf_filtered = vcf_filtered.replace({'chr':''}, regex=True)
+
+vcf_filtered = vcf_filtered.sort_values(by=[0,1])
+
+with open('work1.vcf', 'a') as f:
+    for line in np.array(vcf_filtered):
+        li = str(line).replace('[', '').replace(']', '').replace('\\'', '').replace(' ', '\\t').replace('\\n', '')
+        f.write(f'{li}\\n')
+    " 
+
+     
+    awk '{gsub(/^##contig=<ID=chr/,"##contig=<ID="); print}' work1.vcf > \$workdir/work_2.vcf
+    ###remove non canonical chromososms
+    grep -v '[0-9]_\\|Y_\\|X_\\|Un_' \$workdir/work_2.vcf > \$workdir/work.vcf
+    ###
+    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
+    /home/omic/vcf2prot/bins/Linux/vcf2prot -f \$workdir/annotated.vcf -r /home/omic/vcf2prot/MANE_transcipts_reference.fasta -v -g st -o \$workdir
+
+    mv *.fasta \${patient_name}_transcript_id_mutations.fasta
+    """
+}