Olamide Isreal
bf04f8971e
- Update container image to harbor.cluster.omic.ai/omic/foldseek:latest - Update default paths to /omic/eureka/foldseek/ PVC mount paths - Add k8s profile with eureka-pvc storage - Remove stageInMode copy and containerOptions for k8s compatibility - Update params.json defaults to s3://omic/eureka/foldseek/ paths
144 lines
3.6 KiB
Plaintext
144 lines
3.6 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.query = '/omic/eureka/foldseek/input/1CRN.pdb'
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params.target = '/omic/eureka/foldseek/input/'
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params.outdir = '/omic/eureka/foldseek/output'
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params.mode = 'search'
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params.sensitivity = 9.5
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params.evalue = 0.001
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params.threads = 4
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params.alignment_type = 2
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params.coverage = 0.0
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params.format_output = 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits'
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process FOLDSEEK_SEARCH {
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container 'harbor.cluster.omic.ai/omic/foldseek:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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path query
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path target
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output:
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path "${query.simpleName}_results.m8"
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path "run.log"
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script:
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"""
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foldseek easy-search \\
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${query} \\
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${target} \\
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${query.simpleName}_results.m8 \\
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tmp \\
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--threads ${params.threads} \\
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-s ${params.sensitivity} \\
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-e ${params.evalue} \\
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--alignment-type ${params.alignment_type} \\
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-c ${params.coverage} \\
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--format-output "${params.format_output}" \\
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2>&1 | tee run.log
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rm -rf tmp
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"""
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}
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process FOLDSEEK_CLUSTER {
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container 'harbor.cluster.omic.ai/omic/foldseek:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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path structures
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output:
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path "cluster_cluster.tsv"
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path "cluster_rep_seq.fasta"
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path "cluster_all_seqs.fasta"
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path "run.log"
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script:
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"""
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foldseek easy-cluster \\
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${structures} \\
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cluster \\
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tmp \\
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--threads ${params.threads} \\
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-e ${params.evalue} \\
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--alignment-type ${params.alignment_type} \\
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-c ${params.coverage} \\
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2>&1 | tee run.log
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rm -rf tmp
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"""
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}
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process FOLDSEEK_MULTIMER_SEARCH {
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container 'harbor.cluster.omic.ai/omic/foldseek:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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path query
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path target
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output:
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path "${query.simpleName}_multimer_results.m8"
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path "${query.simpleName}_multimer_results_report"
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path "run.log"
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script:
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"""
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foldseek easy-multimersearch \\
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${query} \\
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${target} \\
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${query.simpleName}_multimer_results \\
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tmp \\
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--threads ${params.threads} \\
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-e ${params.evalue} \\
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2>&1 | tee run.log
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rm -rf tmp
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"""
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}
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process FOLDSEEK_CREATEDB {
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container 'harbor.cluster.omic.ai/omic/foldseek:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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path structures
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output:
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path "structureDB*"
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path "run.log"
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script:
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"""
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foldseek createdb \\
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${structures} \\
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structureDB \\
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--threads ${params.threads} \\
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2>&1 | tee run.log
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"""
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}
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workflow {
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if (params.mode == 'search') {
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query_ch = Channel.fromPath(params.query)
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target_ch = Channel.fromPath(params.target).collect()
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FOLDSEEK_SEARCH(query_ch, target_ch)
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}
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else if (params.mode == 'cluster') {
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structures_ch = Channel.fromPath(params.query).collect()
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FOLDSEEK_CLUSTER(structures_ch)
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}
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else if (params.mode == 'multimersearch') {
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query_ch = Channel.fromPath(params.query)
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target_ch = Channel.fromPath(params.target).collect()
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FOLDSEEK_MULTIMER_SEARCH(query_ch, target_ch)
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}
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else if (params.mode == 'createdb') {
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structures_ch = Channel.fromPath(params.query).collect()
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FOLDSEEK_CREATEDB(structures_ch)
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}
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}
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