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hotfix for _entry.id #13

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hotfix for _entry.id #13

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14 changes: 8 additions & 6 deletions workflow/workflow.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -37,16 +37,16 @@ process runModelCifGenerator {
val entry

output:
path "${entry}-model-${params.version}.cif", emit: cif_file
path "${entry}.cif", emit: cif_file
val entry, emit: entry

script:
"""
echo "Generating model CIF for entry: ${entry}"
${params.python_cmd} run-modelcif-gen \
-p "${params.input_dir}/${getEntryDir(entry)}/${entry}-model-${params.version}.pdb" \
-p "${params.input_dir}/${getEntryDir(entry)}/${entry}.pdb" \
-m "${params.input_dir}/${getEntryDir(entry)}/${entry}-${params.version}.cif.json" \
-o "${entry}-model-${params.version}.cif"
-o "${entry}.cif"
"""
}

Expand All @@ -63,11 +63,12 @@ process runCif2Bcif {

output:
path "${entry}-model-${params.version}.bcif"
path "${entry}-model-${params.version}.cif"

script:
"""
echo "Converting ${entry} CIF to BCIF"
${params.python_cmd} run-cif2bcif -i "${cif_file}" -o "${entry}-model-${params.version}.bcif"
${params.python_cmd} run-cif2bcif -i "${cif_file}" -o "${entry}-model-${params.version}.bcif"
"""
}

Expand All @@ -83,16 +84,17 @@ process runDSSP {
val entry

output:
path "${entry}-model-${params.version}.cif", emit: cif_file
path "${entry}-model-${params.version}.cif", emit: cif_file
val entry, emit: entry

script:
"""
echo "Running DSSP on ${entry} CIF"
${params.python_cmd} run-dssp -i "${cif_file}" -o "${entry}-model-${params.version}.cif"
${params.python_cmd} run-dssp -i "${cif_file}" -o "${entry}-model-${params.version}.cif"
"""
}


params.input_dir = "/input"
params.output_dir = "/output"
params.input_list = "${params.input_dir}/input.txt"
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