From 716f4da68e01baad2bd1b1a1af13c611c6430e95 Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Tue, 11 Aug 2026 16:00:14 +0100 Subject: [PATCH] chore: invoke migrated Jobs via the -i/-o short options MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Seven Jobs call scripts that now build their I/O options from rdkit_utils.add_common_molecule_io_args(). Those scripts accept -i/--infile/--input and -o/--outfile/--output; the long --input and --output spellings are deprecated aliases that will be withdrawn. Switch the affected command blocks to the -i/-o short forms rather than the canonical long spellings. The short forms are canonical too, and they are the only spelling that works against every image these Jobs can be loaded against: informaticsmatters/vs-prep:stable — the tag all of these Jobs pin — was last published in June 2024 and predates the migration, so it has no --infile/--outfile at all. Writing --infile here would make the definitions unloadable until a new image ships; -i/-o has no such ordering dependency and survives the alias removal unchanged. This also matches how squonk2-desc-mordred, squonk2-desc-rdkit and squonk2-train-test-split already invoke their migrated scripts. Job Definition versions are bumped, per docs/versioning.md. Verified with jote against the main manifest: - published vs-prep:stable ..... found=32 passed=32 failed=0 - locally built :latest ........ found=11 passed=11 failed=0 (the 7 changed Jobs, via --image-tag latest) Commands for scripts that never adopted the shared group are untouched: max_min_picker, le_conformers_for_mol, reactor, sucos, fail, prepare_rdock, pharmacophore, convert_file, sdf_manip and the moldb modules all declare --input/--output themselves. The --input/--output on the two nextflow Jobs are workflow params, not script options. Refs InformaticsMatters/squonk2-jobs#39 Co-Authored-By: Claude Opus 5 --- data-manager/im-virtual-screening.yaml | 4 +-- data-manager/rdkit.yaml | 34 +++++++++++++------------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/data-manager/im-virtual-screening.yaml b/data-manager/im-virtual-screening.yaml index b236571..e442d04 100644 --- a/data-manager/im-virtual-screening.yaml +++ b/data-manager/im-virtual-screening.yaml @@ -725,7 +725,7 @@ jobs: name: Enumerate microstates, tautomers and undefined chiral centres description: >- Enumerate microstates, tautomers and undefined chiral centres. - version: '1.0.0' + version: '1.0.1' category: virtual screening keywords: - rdkit @@ -740,7 +740,7 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/enumerate.py --input '{{ inputFile }}' --output '{{ outputFile }}' + /code/enumerate.py -i '{{ inputFile }}' -o '{{ outputFile }}' {% if fragment is defined %}--fragment-method '{{ fragment }}'{% endif %} {% if enumerateCharges is defined and enumerateCharges %}--enumerate-charges{% endif %} {% if enumerateChirals is defined and enumerateChirals %}--enumerate-chirals{% endif %} diff --git a/data-manager/rdkit.yaml b/data-manager/rdkit.yaml index 52ae48e..6e143ed 100644 --- a/data-manager/rdkit.yaml +++ b/data-manager/rdkit.yaml @@ -114,7 +114,7 @@ jobs: generate-low-energy-conformers: name: Generate 3D conformers description: Generate a low energy 3D conformers of molecules - version: '1.0.0' + version: '1.0.1' category: virtual screening keywords: - rdkit @@ -128,7 +128,7 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/le_conformers.py --input '{{ inputFile }}' --output '{{ outputFile }}' + /code/le_conformers.py -i '{{ inputFile }}' -o '{{ outputFile }}' {% if fragment is defined %}--fragment-method '{{ fragment }}'{% endif %} {% if numConformers is defined %}--num-conformers {{ numConformers }}{% endif %} {% if minimizeCycles is defined %}--minimize-cycles {{ minimizeCycles }}{% endif %} @@ -469,7 +469,7 @@ jobs: name: Molecular property calculations description: >- Calculates molecular properties using RDKit - version: '1.0.0' + version: '1.0.1' category: molecular properties keywords: - rdkit @@ -481,8 +481,8 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/rdkit_props.py --input '{{ inputFile }}' - --outfile '{{ outputFile }}' + /code/rdkit_props.py -i '{{ inputFile }}' + -o '{{ outputFile }}' {% if hac is defined and hac %}--hac{% endif %} {% if numRotBonds is defined and numRotBonds %}--num-rot-bonds{% endif %} {% if numRings is defined and numRings %}--num-rings{% endif %} @@ -685,7 +685,7 @@ jobs: name: Deduplicate molecules description: >- Deduplicate molecules using RDKit - version: '1.0.1' + version: '1.0.2' category: molecular properties keywords: - rdkit @@ -697,8 +697,8 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/rdkit_dedup.py --input '{{ inputFile }}' - --outfile '{{ outputFile }}' + /code/rdkit_dedup.py -i '{{ inputFile }}' + -o '{{ outputFile }}' {% if mode is defined and mode %}--mode {{ mode }}{% endif %} {% if minHac is defined %}--min-hac {{ minHac }}{% endif %} {% if maxHac is defined %}--max-hac {{ maxHac }}{% endif %} @@ -828,7 +828,7 @@ jobs: name: Synthetic accessibility score description: >- Calculates a synthetic accessibility score based on the approach of Ertl and Schuffenhauer - version: '1.0.0' + version: '1.0.1' category: molecular properties keywords: - rdkit @@ -841,8 +841,8 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/sa_score.py --input '{{ inputFile }}' - --outfile '{{ outputFile }}' + /code/sa_score.py -i '{{ inputFile }}' + -o '{{ outputFile }}' {% if readHeader is defined and readHeader %}--read-header{% endif %} {% if writeHeader is defined and writeHeader %}--write-header{% endif %} {% if separator is defined %}--delimiter '{{ separator }}'{% endif %} @@ -944,7 +944,7 @@ jobs: Filters molecules by molecular similarity using RDKit. A number of descriptors and metrics are available. Query molecule(s) are specified from a project file or as SMILES. - version: '1.0.0' + version: '1.0.1' category: comp chem keywords: - rdkit @@ -960,9 +960,9 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/screen.py --input '{{ inputFile }}' + /code/screen.py -i '{{ inputFile }}' --queries-file '{{ queries }}' - --output '{{ outputFileName }}' + -o '{{ outputFileName }}' {% if headerInputs is defined %}--read-header{% endif %} {% if headerQueries is defined %}--queries-read-header{% endif %} {% if headerOutputs is defined %}--write-header{% endif %} @@ -1380,7 +1380,7 @@ jobs: name: Butina Clustering description: >- Cluster molecules with Butina and RDKit fingerprints - version: '1.0.0' + version: '1.0.1' category: comp chem keywords: - rdkit @@ -1394,8 +1394,8 @@ jobs: working-directory: /data fix-permissions: true command: >- - /code/cluster_butina.py --input '{{ inputFile }}' - --output {{ outputFile }} + /code/cluster_butina.py -i '{{ inputFile }}' + -o {{ outputFile }} {% if readHeader is defined and readHeader %}--read-header{% endif %} {% if writeHeader is defined and writeHeader %}--write-header{% endif %} {% if separator is defined %}--delimiter {{ separator }}{% endif %}