Configure ImmuneBuilder pipeline for WES execution

- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest - Update input/output paths to S3 (s3://omic/eureka/immunebuilder/) - Remove local mount containerOptions (not needed in k8s) - Update homepage to Gitea repo URL - Clean history to remove large model weight blobs
2026-03-16 15:31:38 +01:00
commit 8887cbe592
49 changed files with 8741 additions and 0 deletions
--- a/main.nf
+++ b/main.nf
@@ -0,0 +1,130 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+params.fasta = 's3://omic/eureka/immunebuilder/antibody_test.fasta'
+params.outdir = 's3://omic/eureka/immunebuilder/output'
+params.mode = 'antibody'
+params.verbose = true
+params.original_weights = false
+
+process ABODYBUILDER2 {
+    container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        path fasta
+
+    output:
+        path "${fasta.simpleName}.pdb", emit: structure
+        path "run.log", emit: logfile
+
+    script:
+        """
+        export HOME=/home/mambauser
+        /opt/conda/bin/ABodyBuilder2 \\
+            -f ${fasta} \\
+            -o ${fasta.simpleName}.pdb \\
+            ${params.verbose ? '-v' : ''} 2>&1 | tee run.log
+        """
+}
+
+process NANOBODYBUILDER2 {
+    container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        path fasta
+
+    output:
+        path "${fasta.simpleName}.pdb", emit: structure
+        path "run.log", emit: logfile
+
+    script:
+        """
+        export HOME=/home/mambauser
+        /opt/conda/bin/NanoBodyBuilder2 \\
+            -f ${fasta} \\
+            -o ${fasta.simpleName}.pdb \\
+            ${params.verbose ? '-v' : ''} 2>&1 | tee run.log
+        """
+}
+
+process TCRBUILDER2 {
+    container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
+    publishDir params.outdir, mode: 'copy'
+    stageInMode 'copy'
+
+    input:
+        path fasta
+
+    output:
+        path "${fasta.simpleName}.pdb", emit: structure
+        path "run.log", emit: logfile
+
+    script:
+        """
+        export HOME=/home/mambauser
+        /opt/conda/bin/TCRBuilder2 \\
+            -f ${fasta} \\
+            -o ${fasta.simpleName}.pdb \\
+            ${params.verbose ? '-v' : ''} \\
+            ${params.original_weights ? '--original_weights' : ''} 2>&1 | tee run.log
+        """
+}
+
+workflow PREDICT_ANTIBODY {
+    take:
+        fasta_ch
+
+    main:
+        ABODYBUILDER2(fasta_ch)
+
+    emit:
+        structure = ABODYBUILDER2.out.structure
+        logfile = ABODYBUILDER2.out.logfile
+}
+
+workflow PREDICT_NANOBODY {
+    take:
+        fasta_ch
+
+    main:
+        NANOBODYBUILDER2(fasta_ch)
+
+    emit:
+        structure = NANOBODYBUILDER2.out.structure
+        logfile = NANOBODYBUILDER2.out.logfile
+}
+
+workflow PREDICT_TCR {
+    take:
+        fasta_ch
+
+    main:
+        TCRBUILDER2(fasta_ch)
+
+    emit:
+        structure = TCRBUILDER2.out.structure
+        logfile = TCRBUILDER2.out.logfile
+}
+
+workflow {
+    if (!params.fasta) {
+        error "Please provide input FASTA file(s) using --fasta parameter"
+    }
+
+    fasta_ch = Channel.fromPath(params.fasta, checkIfExists: true)
+
+    if (params.mode == 'antibody') {
+        PREDICT_ANTIBODY(fasta_ch)
+    } else if (params.mode == 'nanobody') {
+        PREDICT_NANOBODY(fasta_ch)
+    } else if (params.mode == 'tcr') {
+        PREDICT_TCR(fasta_ch)
+    } else {
+        error "Invalid mode: ${params.mode}. Please use 'antibody', 'nanobody', or 'tcr'"
+    }
+}