update from upstream asbc-bindflow/main

conf/gadi.config

@@ -17,6 +17,9 @@ params {
     use_dgxa100                 = false
 }
 
+env.OPENMM_PLATFORM_ORDER="CPU"
+env.OPENMM_DEFAULT_PLATFORM="CPU"
+
 process {
     executor = "pbspro"
     storage = "gdata/if89+scratch/${params.project}+gdata/${params.project}"

conf/modules.config

@@ -31,7 +31,7 @@ process {
     withName: 'JSONMANAGER' {
         memory = 2.GB
         time   = 1.h
-        ext.args2 = "${params.quote_char}"
+        //ext.args2 = "${params.quote_char}"
     }
 
     withName: 'RANKER' {
@@ -42,6 +42,7 @@ process {
     withName: 'BINDCRAFT' {
         container = "${params.bindcraft_container}"
         memory = 24.GB
+        time = 24.h
         errorStrategy = params.error_strategy ?: "terminate"
         afterScript = {
             def output_path = new File("${params.outdir}")

docker/Dockerfile

@@ -0,0 +1,42 @@
+# Use the latest official Ubuntu image from Docker Hub
+FROM mambaorg/micromamba:2.3.3
+LABEL maintainer="Ziad Al Bkhetan <ziad.albkhetan@gmail.come>"
+LABEL version="1.0.3"
+LABEL description="A Docker image for running Free Bindcraft "
+LABEL org.opencontainers.image.authors="Ziad Al Bkhetan"
+LABEL org.opencontainers.image.licenses="MIT"
+
+# Prevent interactive prompts during package installation
+ENV DEBIAN_FRONTEND=noninteractive
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+WORKDIR /
+USER root
+RUN mkdir -p /work && chown -R mambauser:mambauser /work
+USER mambauser
+WORKDIR /work
+RUN micromamba install -y -n base -c conda-forge git wget gcc && micromamba clean -a -y
+RUN git clone --branch v1.0.3 --depth 1 https://github.com/cytokineking/FreeBindCraft
+WORKDIR FreeBindCraft
+
+# making it work for micromamba by replacing conda by micromamba and installing to the base env
+
+RUN sed -i '/\$pkg_manager create --name BindCraft/s/^/#/' install_bindcraft.sh
+RUN sed -i '/conda env list | grep -w/s/^/#/' install_bindcraft.sh
+RUN sed -i '/source ${CONDA_BASE}\/bin\/activate/s/^/#/' install_bindcraft.sh
+RUN sed -i '/[[:space:]]*\[ "\$CONDA_DEFAULT_ENV" = "BindCraft" \]/s/^/#/' install_bindcraft.sh
+RUN sed -i 's/\<conda\>/micromamba/g' install_bindcraft.sh
+RUN sed -i 's/\<micromamba-forge\>/conda-forge/g' install_bindcraft.sh
+
+RUN bash install_bindcraft.sh --cuda '12.4' --pkg_manager 'micromamba' --no-pyrosetta
+ENV PATH="$PATH:/work/FreeBindCraft"
+USER root
+RUN apt-get update && apt-get install -y --no-install-recommends procps && rm -rf /var/lib/apt/lists/*
+USER mambauser
+RUN micromamba install -y -n base -c conda-forge ffmpeg && \
+    micromamba clean -a -y
+ENV PATH=/opt/conda/bin:$PATH
+ENV PYTHONPATH="/work/FreeBindCraft"
+
+# Set default command
+CMD ["python", "-u", "bindcraft.py"]

docker/Dockerfile-1

@@ -0,0 +1,105 @@
+# This Dockerfile was adapted from the below to create a bindcraft container by Uwe Winter <uwe@biocommons.org.au>
+# This Dockerfile was adapted for running on Azure CycleCloud by Felipe Ayora
+# (bizdata.co.nz)
+
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Look for latest version that matches NVIDIA drivers on the Azure GPU machines:
+#   https://hub.docker.com/r/nvidia/cuda/tags?page=1&name=cudnn8-runtime-ubuntu18
+
+# Build image:
+# 1. Run:
+#       git clone https://github.com/deepmind/alphafold/releases/tag/vx.x.x
+#       cd ./alphafold
+# 2. Run:
+#       sudo docker build -t <repo/tag:version> -f ./path/to/this/Dockerfile .
+
+ARG CUDA=12.4.1
+FROM nvidia/cuda:${CUDA}-cudnn-runtime-ubuntu22.04
+
+# Remove entrypoint messaging to stdout
+RUN rm /opt/nvidia/entrypoint.d/*
+
+# FROM directive resets ARGS, so we specify again
+
+ARG CUDA_MAJOR=12
+ARG CUDACMDTOOLS=12.4
+
+# Use bash to support string substitution.
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y  --no-install-recommends \
+      build-essential \
+      cmake \
+      cuda-command-line-tools-${CUDACMDTOOLS/./-} \
+      wget \
+      git \
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get autoremove -y \
+    && apt-get clean
+
+# Install Miniconda package manager.
+RUN wget -q -P /tmp \
+  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+
+# Install conda packages.
+ENV PATH="/opt/conda/bin:$PATH"
+
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
+COPY bindcraft /app/
+RUN chmod +x /app/install_bindcraft.sh
+
+WORKDIR /app/
+RUN /app/install_bindcraft.sh --cuda 12.4.1 --pkg_manager 'conda'
+
+# Install pip packages.
+
+# Add SETUID bit to the ldconfig binary so that non-root users can run it.
+RUN chmod u+s /sbin/ldconfig.real
+
+# properly configure ldconfig and run it
+RUN echo "/opt/conda/lib" > /etc/ld.so.conf.d/conda.conf \
+    && echo "/opt/conda/envs/BindCraft/lib" >> /etc/ld.so.conf.d/conda.conf \
+    && ldconfig
+
+# ENTRYPOINT does not support easily running multiple commands, so instead we
+# write a shell script to wrap them up.
+# We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
+# with Debian. See https://github.com/NVIDIA/nvidia-docker/issues/1399 for
+# details.
+RUN printf '#!/bin/bash\n\
+ldconfig\n\
+__conda_setup="$('/opt/conda/bin/conda' '\''shell.bash'\'' '\''hook'\'' 2> /dev/null)"\n\
+if [ $? -eq 0 ]; then\n\
+    eval "$__conda_setup"\n\
+else\n\
+    if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then\n\
+        . "/opt/conda/etc/profile.d/conda.sh"\n\
+    else\n\
+        export PATH="/opt/conda/bin:$PATH"\n\
+    fi\n\
+fi\n\
+unset __conda_setup\n\
+conda activate BindCraft\n\
+python -u /app/bindcraft.py "$@"\n' > /app/run_bindcraft.sh \
+  && chmod +x /app/run_bindcraft.sh
+
+# Removed entry point to facilitate running via Galaxy bash scripts
+ENTRYPOINT ["/app/run_bindcraft.sh"]

docs/usage.md

@@ -14,7 +14,7 @@
 
 `outdir`: the output directory where the results will be stored.
 
-`bindcraft_container`: the path to bindcraft container that is needed run the workflow.
+`bindcraft_container`: the path to bindcraft container that is needed run the workflow. By default, teh workflow uses n open source version of Bindcraft ([FreeBindCraft](https://github.com/cytokineking/FreeBindCraft)) that is is hosted at Docker hub ([freebindcraft:1.0.3](https://hub.docker.com/r/australianbiocommons/freebindcraft)).
 
 ### Optional
 

modules/local/bindcraft/main.nf

@@ -12,6 +12,10 @@ process BINDCRAFT {
         tuple val(meta), path("*_output/Accepted/Ranked"), emit: accepted_ranked
         tuple val(meta), path("*_output/Accepted/*pdb"), emit: accepted
         tuple val(meta), path("*_output"), emit: output_dir
+        tuple val(meta), path("*_output/failure_csv.csv") , emit: failure_csv
+        tuple val(meta), path("*_output/final_design_stats.csv"), emit: final_design_stats
+        tuple val(meta), path("*_output/mpnn_design_stats.csv"), emit: mpnn_design_stats
+        tuple val(meta), path("*_output/trajectory_stats.csv"), emit: trajectory_stats
         path "versions.yml", emit: versions
 
     when:
@@ -22,7 +26,7 @@ process BINDCRAFT {
     def args = task.ext.args ?: ''
 
     """
-    /app/run_bindcraft.sh \\
+    python /work/FreeBindCraft/bindcraft.py \\
         --settings ${target_file} \\
         --filters ${filters} \\
         --advanced ${advanced_settings} \\

modules/local/generate_report.nf

@@ -0,0 +1,51 @@
+process GENERATE_REPORT {
+    tag "all-run"
+    label 'process_single'
+    container 'ghcr.io/australian-protein-design-initiative/containers/nf-binder-design-utils:0.1.5'
+
+    input:
+    // Stage all batch result directories under ./batches/{n}/
+    // Note the {n} in this case is a list index and may not match the batch_id
+    // For the purposes of generating aggregate stats, the batch_id is not important
+    path ('batches/*')
+    path('failure_csv.csv')
+    path('final_design_stats.csv')
+    path('mpnn_design_stats.csv')
+    path('trajectory_stats.csv')
+    path (qmd_template)
+
+    output:
+    path('bindcraft_report.html'), emit: report
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    export XDG_CACHE_HOME="./.cache"
+    export XDG_DATA_HOME="./.local/share"
+    export JUPYTER_RUNTIME_DIR="./.jupyter"
+    export XDG_RUNTIME_DIR="/tmp"
+
+    quarto render ${qmd_template} \\
+    --execute-dir \${PWD} \\
+    --output - > bindcraft_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        quarto: \$(quarto --version)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+
+    touch bindcraft_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        quarto: \$(quarto --version)
+    END_VERSIONS
+    """
+}

nextflow.config

@@ -17,7 +17,7 @@ params {
     settings_advanced = null
     batches = 1
     quote_char = "\""
-    bindcraft_container = null
+    bindcraft_container = "australianbiocommons/freebindcraft:1.0.3"
 
     // MultiQC options
     multiqc_config             = null
@@ -186,14 +186,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

nextflow_schema.json

@@ -52,8 +52,6 @@
             "properties": {
                 "bindcraft_container": {
                     "type": "string",
-                    "format": "file-path",
-                    "exists": true,
                     "description": "Path to bindcraft container to be used during execution.",
                     "help_text": "",
                     "fa_icon": "fas fa-file-csv"

subworkflows/local/run_bindcraft.nf

@@ -12,6 +12,8 @@ include { JSONMANAGER               } from '../../modules/local/jsonmanager'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { BINDCRAFT                 } from '../../modules/local/bindcraft'
 include { RANKER                 } from '../../modules/local/ranker'
+include { GENERATE_REPORT        } from '../../modules/local/generate_report'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
@@ -83,6 +85,34 @@ workflow RUN_BINDCRAFT {
         BINDCRAFT.out.accepted_ranked.map{[["id": it[0].id], it[1]]}.groupTuple()
     )
 
+    GENERATE_REPORT(
+        BINDCRAFT.out.output_dir.map{it[1]}.collect(),
+        BINDCRAFT.out.failure_csv
+            .map{it[1]}
+            .splitCsv( header: true )
+            .collect()
+            .map{
+                it.inject([:]) { acc, map ->
+                    map.each { k, v ->
+                        def num = v?.toString()?.isNumber() ? v.toBigDecimal() : 0
+                        acc[k] = (acc[k] ?: 0) + num
+                }
+                def keys = acc.keySet().toList()
+                def values = keys.collect { acc[it] }
+                keys.join(',') + "\n" + values.join(',')
+                }
+            }.collectFile( name: "failure_csv.csv")
+            ,
+        RANKER.out.stats.map{it[1]},
+        BINDCRAFT.out.mpnn_design_stats
+        .map{it[1].text}
+        .collectFile( name: "mpnn_design_stats.csv" ),
+        BINDCRAFT.out.trajectory_stats
+        .map{it[1].text}
+        .collectFile( name: "trajectory_stats.csv" ),
+        Channel.fromPath("${projectDir}/assets/bindcraft_reporting.qmd").first()
+    )
+
     emit:
     input_json  = JSONMANAGER.out.json
                     .flatten()
@@ -93,6 +123,7 @@ workflow RUN_BINDCRAFT {
     output_dir  = BINDCRAFT.out.output_dir
     stats       = RANKER.out.stats
     ranked      = RANKER.out.accepted_ranked
+    reports     = GENERATE_REPORT.out.report
     versions    = ch_versions
 }
 

subworkflows/local/utils_nfcore_bindflow_pipeline/main.nf

@@ -223,5 +223,5 @@ def validateInputParameters() {
 // Print a warning when using Bindcraft
 //
 def checkBindcraftContainer() {
-    log.warn "You need to provide a valid path for the singularity/Docker container! or bindcraft needs to be avaialble on the system!"
+    error ("You need to provide a valid path for the singularity/Docker container! or bindcraft needs to be avaialble on the system!")
 }

tower.yml

@@ -1,5 +1,8 @@
 reports:
-  multiqc_report.html:
-    display: "MultiQC HTML report"
+  "*_report.html":
+    display: "HTML report"
   samplesheet.csv:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"
+  "*_final_design_stats.csv":
+    display: "Stats and Ranking"
+

workflows/bindflow.nf

@@ -34,6 +34,7 @@ workflow BINDFLOW {
         ch_batches,
         quote_char
     )
+
     //
     // Collate and save software versions
     //