separated expansion from remainder of workflow

Author: tdudgeon

data/mpro/hits-23.sdf.gz

@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+// expand params
+params.hits = 'data/mpro/hits-5.sdf.gz'
+params.token = null
+params.hac_min = 3
+params.hac_max = 3
+params.rac_min = 1
+params.rac_max = 1
+params.hops = 1
+params.server = null
+
+
+// files
+hits = file(params.hits)
+
+process fragnet_expand {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    publishDir ".", mode: 'copy'
+
+    input:
+    file hits
+
+    output:
+    file '*.smi' into smiles
+    file '*.mol' into mols
+
+    """
+    python -m pipelines.xchem.fragnet_expand -i '$hits' ${params.token ? '--token ' + params.token : ''}\
+      --hops $params.hops\
+      --hac-min $params.hac_min\
+      --hac-max $params.hac_max\
+      --rac-min $params.rac_min\
+      --rac-max $params.rac_max\
+      ${params.server ? '--server ' + params.server : ''}
+    """
+}

src/nextflow/xchem/expand.nf

@@ -0,0 +1,146 @@
+#!/usr/bin/env nextflow
+
+// splitter params
+params.chunk_size_expand = 200
+params.limit = 0
+params.digits = 4
+
+// tether params
+params.smiles = '*.smi'
+params.molfiles = '*.mol'
+params.ph_min = null
+params.ph_max = null
+params.timeout_embed = null
+params.chunk_size_tether =  null
+
+// docking params
+params.protein = 'data/mpro/Mpro-x0387_0.mol2'
+params.prmfile = 'data/mpro/docking-tethered.prm'
+params.asfile = 'data/mpro/docking-tethered.as'
+params.num_dockings = 5
+
+// featurestein
+params.fragments = 'data/mpro/hits-23.sdf.gz'
+
+// files
+smiles = file(params.smiles)
+molfiles = file(params.molfiles)
+protein = file(params.protein)
+prmfile = file(params.prmfile)
+asfile = file(params.asfile)
+fragments = file(params.fragments)
+
+
+process splitter {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    input:
+    file smiles from smiles.flatten()
+    file mol from molfiles.flatten()
+
+    output:
+    file '*.mol' into split_mols
+    file '*.smi' into split_smiles
+
+    """
+    stem=${smiles.name[0..-5]}
+    split -l $params.chunk_size_expand -d -a 3 --additional-suffix .smi $smiles \${stem}_
+    mv $smiles ${smiles}.orig
+    for f in *.smi
+    do
+      cp $mol \${f:0:-4}.mol
+    done
+    mv $mol ${mol}.orig
+    """
+}
+
+
+process tether {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    input:
+    file mol from split_mols.flatten()
+    file smiles from split_smiles.flatten()
+
+    output:
+    file 'Tethered_*.sdf' into tethered_parts
+
+    """
+    python -m pipelines.xchem.prepare_tether --smi '$smiles' --mol '$mol'\
+      ${params.ph_min != null ? '--min-ph ' + params.ph_min : ''}\
+      ${params.ph_max != null ? '--max-ph ' + params.ph_max : ''}\
+      ${params.timeout_embed != null ? '--timeout-embed ' + params.timeout_embed : ''}\
+      -o 'Tethered_${smiles.name[0..-5]}'
+    """
+}
+
+process rdock {
+
+    container 'informaticsmatters/rdock-mini:latest'
+    errorStrategy 'retry'
+    maxRetries 3
+
+	input:
+    file part from tethered_parts.flatten()
+	file 'receptor.mol2' from protein
+	file 'docking.prm' from prmfile
+	file 'docking.as' from asfile
+
+    output:
+    file 'Docked_*.sd' into docked_parts
+
+    """
+    rbdock -r $prmfile -p dock.prm -n $params.num_dockings -i $part -o ${part.name.replace('Tethered', 'Docked')[0..-5]} > docked_out.log
+    """
+}
+
+process gen_feat_maps {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    input:
+    file fragments
+
+    output:
+    file 'featurestein.p' into fmaps
+
+    """
+    python -m pipelines.xchem.featurestein_generate -i '$fragments' -f featurestein.p
+    """
+}
+
+process featurestein {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+	input:
+    file part from docked_parts
+    file fmaps
+
+    output:
+    file 'FS_*.sdf' into featurestein_parts
+
+    """
+    python -m pipelines.xchem.featurestein_score -i '$part' -if sdf -f '$fmaps' -o 'FS_${part.name[0..-4]}' -of sdf --no-gzip
+    """
+}
+
+process xcos {
+
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    publishDir ".", mode: 'move'
+
+	input:
+    file part from featurestein_parts
+    file fragments
+
+    output:
+    file 'XC_*.sdf'
+
+    """
+    python -m pipelines.xchem.xcos -i '$part' -if sdf -f '$hits' -o 'XC_${part.name[0..-5]}' -of sdf --no-gzip
+    """
+}