From 53de0513516991d4de0c5df38ff277be39690f40 Mon Sep 17 00:00:00 2001 From: meesters Date: Wed, 6 Aug 2025 14:10:08 +0200 Subject: [PATCH 01/15] feat: added conda env for histograms --- workflow/envs/histogram.yml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 workflow/envs/histogram.yml diff --git a/workflow/envs/histogram.yml b/workflow/envs/histogram.yml new file mode 100644 index 0000000..961f3af --- /dev/null +++ b/workflow/envs/histogram.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python>=3.12.4 + - pandas>=2.2.2 \ No newline at end of file From c3e631701af3ae7001c69c8871c4d4c395868359 Mon Sep 17 00:00:00 2001 From: meesters Date: Wed, 6 Aug 2025 14:26:24 +0200 Subject: [PATCH 02/15] feat: added conda specs to some rules --- workflow/envs/biopython.yml | 7 +++++++ workflow/envs/openbabel.yml | 4 ++++ workflow/envs/{histogram.yml => simple_pandas.yml} | 0 workflow/rules/analyse.smk | 6 ++++++ workflow/rules/preparation.smk | 10 ++++++++++ 5 files changed, 27 insertions(+) create mode 100644 workflow/envs/biopython.yml create mode 100644 workflow/envs/openbabel.yml rename workflow/envs/{histogram.yml => simple_pandas.yml} (100%) diff --git a/workflow/envs/biopython.yml b/workflow/envs/biopython.yml new file mode 100644 index 0000000..200df86 --- /dev/null +++ b/workflow/envs/biopython.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - python>=3.12.4 + - biopython >=1.84 + - pandas>=2.2.2 \ No newline at end of file diff --git a/workflow/envs/openbabel.yml b/workflow/envs/openbabel.yml new file mode 100644 index 0000000..c9493cb --- /dev/null +++ b/workflow/envs/openbabel.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - openbabel>=3.1.1 \ No newline at end of file diff --git a/workflow/envs/histogram.yml b/workflow/envs/simple_pandas.yml similarity index 100% rename from workflow/envs/histogram.yml rename to workflow/envs/simple_pandas.yml diff --git a/workflow/rules/analyse.smk b/workflow/rules/analyse.smk index eb7b05c..5f948c7 100644 --- a/workflow/rules/analyse.smk +++ b/workflow/rules/analyse.smk @@ -172,6 +172,8 @@ rule makeHistogram: ), log: "logs/makeHistogram_{receptorID}.log", + conda: + "../envs/simple_pandas.yml" envmodules: config["PYPLOT"], script: @@ -214,6 +216,8 @@ rule dockingResultsTxt: path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"), log: "logs/dockingResultsTxt_{receptorID}_{percentage}.log", + conda: + "../envs/simple_pandas.yml" wildcard_constraints: receptorID="[^/]+", percentage="[^/]+", @@ -420,6 +424,8 @@ rule makeVenn: ), category="Rescreening", ), + conda: + "../envs/simple_pandas.yml" log: "logs/makeVenn_{receptorID}_{percentage}.log", script: diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 303b2b8..7c67023 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -32,6 +32,8 @@ rule convertMol2: path.join(INPUT_DIR, "ZINC", "subsets", "{subset}.mol2"), output: path.join(TMP_DIR, "unzipped", "ZINC", "subsets", "{subset}.pdbqt"), + conda: + "../envs/openbabel.yml" envmodules: config["OPENBABEL"], shell: @@ -64,6 +66,8 @@ rule SDFToPDBQT: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.sdf"), output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.pdbqt"), + conda: + "../envs/openbabel.yml" envmodules: config["OPENBABEL"], shell: @@ -75,6 +79,8 @@ rule prepareReceptor: path.join(TMP_DIR, "unzipped", "PDB", "receptor", "{name}.pdb"), output: path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"), + conda: + "../envs/biopython.yml" envmodules: config["BIOPYTHON"], script: @@ -86,6 +92,8 @@ rule makeReceptorPDBQT: path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"), output: path.join(PREPARED_DIR, "receptor", "{name}.pdbqt"), + conda: + "../envs/openbabel.yml" envmodules: config["OPENBABEL"], shell: @@ -138,6 +146,8 @@ rule energyMin: partition=config["ENERGY_MIN"]["partition"], runtime=config["ENERGY_MIN"]["runtime"], mem_mb=config["ENERGY_MIN"]["mem_mb"], + conda: + "../envs/openbabel.yml" envmodules: config["OPENBABEL"], shell: From 28a9c110ef1fe31989d35aff9cf85855f8b35b62 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 09:45:51 +0200 Subject: [PATCH 03/15] added conda envs --- workflow/envs/basic.yml | 0 workflow/envs/biopython.yml | 4 ++++ workflow/envs/openbabel.yml | 4 ++++ workflow/envs/plotting.yml | 5 +++++ workflow/envs/vinalc.yml | 4 ++++ workflow/rules/analyse.smk | 15 ++++++++++----- workflow/rules/docking.smk | 2 ++ workflow/rules/preparation.smk | 20 ++++++++++++++++++-- 8 files changed, 47 insertions(+), 7 deletions(-) create mode 100644 workflow/envs/basic.yml create mode 100644 workflow/envs/biopython.yml create mode 100644 workflow/envs/openbabel.yml create mode 100644 workflow/envs/plotting.yml create mode 100644 workflow/envs/vinalc.yml diff --git a/workflow/envs/basic.yml b/workflow/envs/basic.yml new file mode 100644 index 0000000..e69de29 diff --git a/workflow/envs/biopython.yml b/workflow/envs/biopython.yml new file mode 100644 index 0000000..1ba2c96 --- /dev/null +++ b/workflow/envs/biopython.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - biopython>=1.85 \ No newline at end of file diff --git a/workflow/envs/openbabel.yml b/workflow/envs/openbabel.yml new file mode 100644 index 0000000..abc1815 --- /dev/null +++ b/workflow/envs/openbabel.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - openbabel>=3.1.1 \ No newline at end of file diff --git a/workflow/envs/plotting.yml b/workflow/envs/plotting.yml new file mode 100644 index 0000000..4ee8ded --- /dev/null +++ b/workflow/envs/plotting.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge +dependencies: + - matplotlib>=3.10.6 + - venn>=0.1.3 \ No newline at end of file diff --git a/workflow/envs/vinalc.yml b/workflow/envs/vinalc.yml new file mode 100644 index 0000000..ccd128c --- /dev/null +++ b/workflow/envs/vinalc.yml @@ -0,0 +1,4 @@ +channels: + - bioconda +dependencies: + - vinalc>=1.4.2 \ No newline at end of file diff --git a/workflow/rules/analyse.smk b/workflow/rules/analyse.smk index eb7b05c..81e4001 100644 --- a/workflow/rules/analyse.smk +++ b/workflow/rules/analyse.smk @@ -172,6 +172,8 @@ rule makeHistogram: ), log: "logs/makeHistogram_{receptorID}.log", + conda: + "../envs/plotting.yml", envmodules: config["PYPLOT"], script: @@ -277,11 +279,10 @@ rule prepareSecondDocking: ), log: "logs/prepareSecondDocking_{name}_{receptorID}_{percentage}.log", - shell: - """ - cp {input.grid} {output.grid} - echo {input.receptor} > {output.receptor} - """ + run: + import shutil + shutil.copy(input.grid, output.grid) + shutil.copy(input.receptor, output.receptor) rule docking2: @@ -314,6 +315,8 @@ rule docking2: tasks=config["DOCKING"]["ntasks"], slurm_extra=config["DOCKING"]["slurm_extra"], runtime=config["DOCKING"]["runtime"], + conda: + "../envs/vinalc.yml", envmodules: config["VINALC"], shell: @@ -422,5 +425,7 @@ rule makeVenn: ), log: "logs/makeVenn_{receptorID}_{percentage}.log", + conda: + "../envs/plotting.yml", script: "../scripts/union_venn.py" diff --git a/workflow/rules/docking.smk b/workflow/rules/docking.smk index c1ed1ac..92d4c06 100644 --- a/workflow/rules/docking.smk +++ b/workflow/rules/docking.smk @@ -27,6 +27,8 @@ rule docking: "{dataset}", "{receptorID}.txt_{database}_{dataset}_{name}_{i}.txt.pdbqt.gz", ), + conda: + "../envs/vinalc.yml", envmodules: config["VINALC"], params: diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 303b2b8..f8f87bd 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -32,6 +32,8 @@ rule convertMol2: path.join(INPUT_DIR, "ZINC", "subsets", "{subset}.mol2"), output: path.join(TMP_DIR, "unzipped", "ZINC", "subsets", "{subset}.pdbqt"), + conda: + "../envs/openbabel.yml", envmodules: config["OPENBABEL"], shell: @@ -43,6 +45,8 @@ rule mergeLocalInput: in_dir=LOCAL_INPUT, output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "local.pdbqt"), + conda: + "../envs/openbabel.yml", envmodules: config["OPENBABEL"], script: @@ -64,6 +68,8 @@ rule SDFToPDBQT: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.sdf"), output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.pdbqt"), + conda: + "../envs/openbabel.yml", envmodules: config["OPENBABEL"], shell: @@ -75,6 +81,8 @@ rule prepareReceptor: path.join(TMP_DIR, "unzipped", "PDB", "receptor", "{name}.pdb"), output: path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"), + conda: + "../envs/biopython.yml", envmodules: config["BIOPYTHON"], script: @@ -86,6 +94,8 @@ rule makeReceptorPDBQT: path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"), output: path.join(PREPARED_DIR, "receptor", "{name}.pdbqt"), + conda: + "../envs/openbabel.yml", envmodules: config["OPENBABEL"], shell: @@ -97,6 +107,8 @@ rule gunzip: path.join(INPUT_DIR, "{database}", "{dataset}", "{name}.{filetype}.gz"), output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.{filetype}"), + conda: + "../basic.yml", shell: "gunzip < {input} > {output} || touch {output}" @@ -138,6 +150,8 @@ rule energyMin: partition=config["ENERGY_MIN"]["partition"], runtime=config["ENERGY_MIN"]["runtime"], mem_mb=config["ENERGY_MIN"]["mem_mb"], + conda: + "../envs/openbabel.yml", envmodules: config["OPENBABEL"], shell: @@ -167,5 +181,7 @@ rule prepareDocking: path.join(PREPARED_DIR, "receptor", "{receptorID}.pdbqt"), output: path.join(OUTPUT_DIR, "receptor", "{receptorID}.txt"), - shell: - "echo {input} > {output}" + run: + import shutil + shutil.copy(input[0], output[0]) + From 37a62acf1f44327734be7accd68c9ae5b69ef0d6 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 10:18:21 +0200 Subject: [PATCH 04/15] fix: formatting --- workflow/rules/analyse.smk | 13 +++------- workflow/rules/preparation.smk | 46 ++++++++++++++++------------------ 2 files changed, 25 insertions(+), 34 deletions(-) diff --git a/workflow/rules/analyse.smk b/workflow/rules/analyse.smk index fecf287..2cb9e3b 100644 --- a/workflow/rules/analyse.smk +++ b/workflow/rules/analyse.smk @@ -173,11 +173,7 @@ rule makeHistogram: log: "logs/makeHistogram_{receptorID}.log", conda: -<<<<<<< HEAD - "../envs/simple_pandas.yml" -======= - "../envs/plotting.yml", ->>>>>>> main + "../envs/plotting.yml" envmodules: config["PYPLOT"], script: @@ -287,6 +283,7 @@ rule prepareSecondDocking: "logs/prepareSecondDocking_{name}_{receptorID}_{percentage}.log", run: import shutil + shutil.copy(input.grid, output.grid) shutil.copy(input.receptor, output.receptor) @@ -322,7 +319,7 @@ rule docking2: slurm_extra=config["DOCKING"]["slurm_extra"], runtime=config["DOCKING"]["runtime"], conda: - "../envs/vinalc.yml", + "../envs/vinalc.yml" envmodules: config["VINALC"], shell: @@ -430,10 +427,8 @@ rule makeVenn: category="Rescreening", ), conda: - "../envs/simple_pandas.yml" + "../envs/plotting.yml" log: "logs/makeVenn_{receptorID}_{percentage}.log", - conda: - "../envs/plotting.yml", script: "../scripts/union_venn.py" diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 0440d90..b9acbb6 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -33,11 +33,7 @@ rule convertMol2: output: path.join(TMP_DIR, "unzipped", "ZINC", "subsets", "{subset}.pdbqt"), conda: -<<<<<<< HEAD "../envs/openbabel.yml" -======= - "../envs/openbabel.yml", ->>>>>>> main envmodules: config["OPENBABEL"], shell: @@ -50,7 +46,7 @@ rule mergeLocalInput: output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "local.pdbqt"), conda: - "../envs/openbabel.yml", + "../envs/openbabel.yml" envmodules: config["OPENBABEL"], script: @@ -73,11 +69,7 @@ rule SDFToPDBQT: output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.pdbqt"), conda: -<<<<<<< HEAD "../envs/openbabel.yml" -======= - "../envs/openbabel.yml", ->>>>>>> main envmodules: config["OPENBABEL"], shell: @@ -90,11 +82,7 @@ rule prepareReceptor: output: path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"), conda: -<<<<<<< HEAD "../envs/biopython.yml" -======= - "../envs/biopython.yml", ->>>>>>> main envmodules: config["BIOPYTHON"], script: @@ -107,11 +95,7 @@ rule makeReceptorPDBQT: output: path.join(PREPARED_DIR, "receptor", "{name}.pdbqt"), conda: -<<<<<<< HEAD "../envs/openbabel.yml" -======= - "../envs/openbabel.yml", ->>>>>>> main envmodules: config["OPENBABEL"], shell: @@ -124,7 +108,7 @@ rule gunzip: output: path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.{filetype}"), conda: - "../basic.yml", + "../envs/basic.yml" shell: "gunzip < {input} > {output} || touch {output}" @@ -167,11 +151,7 @@ rule energyMin: runtime=config["ENERGY_MIN"]["runtime"], mem_mb=config["ENERGY_MIN"]["mem_mb"], conda: -<<<<<<< HEAD "../envs/openbabel.yml" -======= - "../envs/openbabel.yml", ->>>>>>> main envmodules: config["OPENBABEL"], shell: @@ -183,8 +163,24 @@ rule prepareGeometry: path.join(config["GRID_DIR"], "{receptorID}.gpf"), output: path.join(OUTPUT_DIR, "grid", "{receptorID}_grid.txt"), - shell: - "egrep 'npts|gridcenter' {input} |cut -f2-4 -d' '| tac |tr '\n' ' ' > {output} && sed -i -e '$a\ ' {output}" + run: + grid_params = [] + + with open(input[0], "r") as f: + for line in f: + # Match lines starting with 'npts' or 'gridcenter' + if line.startswith(("npts", "gridcenter")): + # Extract fields 2-4 (space-separated values after the first field) + parts = line.strip().split() + if len(parts) >= 4: + grid_params.append(" ".join(parts[1:4])) + + # Reverse the order (equivalent to 'tac') + grid_params.reverse() + + # Write to output file with space separation and trailing newline + with open(output[0], "w") as f: + f.write(" ".join(grid_params) + " \n") rule prepareLibrary: @@ -203,5 +199,5 @@ rule prepareDocking: path.join(OUTPUT_DIR, "receptor", "{receptorID}.txt"), run: import shutil - shutil.copy(input[0], output[0]) + shutil.copy(input[0], output[0]) From 8df159a14f93cd47b54e983d92d5f66e29735df4 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 10:19:01 +0200 Subject: [PATCH 05/15] fix: formatting --- workflow/rules/docking.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/docking.smk b/workflow/rules/docking.smk index 92d4c06..1470c85 100644 --- a/workflow/rules/docking.smk +++ b/workflow/rules/docking.smk @@ -28,7 +28,7 @@ rule docking: "{receptorID}.txt_{database}_{dataset}_{name}_{i}.txt.pdbqt.gz", ), conda: - "../envs/vinalc.yml", + "../envs/vinalc.yml" envmodules: config["VINALC"], params: From 8c5081a1e1b386bdf86b1e80cb6ec98a3317efd6 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 10:59:18 +0200 Subject: [PATCH 06/15] fix: formatting --- workflow/rules/preparation.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index b9acbb6..4598371 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -175,7 +175,7 @@ rule prepareGeometry: if len(parts) >= 4: grid_params.append(" ".join(parts[1:4])) - # Reverse the order (equivalent to 'tac') + # Reverse the order (equivalent to 'tac') grid_params.reverse() # Write to output file with space separation and trailing newline From 88d4316934a0bad15ef574633ad9a4e82b974ab3 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:08:13 +0200 Subject: [PATCH 07/15] fix: formatting - not logical --- workflow/rules/preparation.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 4598371..b9acbb6 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -175,7 +175,7 @@ rule prepareGeometry: if len(parts) >= 4: grid_params.append(" ".join(parts[1:4])) - # Reverse the order (equivalent to 'tac') + # Reverse the order (equivalent to 'tac') grid_params.reverse() # Write to output file with space separation and trailing newline From 4cc0753227c6d2fc3d2b01be64d36ed631f83cec Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:13:17 +0200 Subject: [PATCH 08/15] Update workflow/rules/preparation.smk Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- workflow/rules/preparation.smk | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index b9acbb6..2e634a7 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -197,7 +197,5 @@ rule prepareDocking: path.join(PREPARED_DIR, "receptor", "{receptorID}.pdbqt"), output: path.join(OUTPUT_DIR, "receptor", "{receptorID}.txt"), - run: - import shutil - - shutil.copy(input[0], output[0]) + shell: + "echo {input} > {output}" From 39a1f6b255c117833be1eedd4c66f26eacb44819 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:18:53 +0200 Subject: [PATCH 09/15] fix: merge conflict --- workflow/envs/biopython.yml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/workflow/envs/biopython.yml b/workflow/envs/biopython.yml index ad496db..1ba2c96 100644 --- a/workflow/envs/biopython.yml +++ b/workflow/envs/biopython.yml @@ -1,13 +1,4 @@ channels: -<<<<<<< HEAD - - conda-forge - - bioconda -dependencies: - - python>=3.12.4 - - biopython >=1.84 - - pandas>=2.2.2 -======= - conda-forge dependencies: - - biopython>=1.85 ->>>>>>> main + - biopython>=1.85 \ No newline at end of file From 2ff403705752ce6f336a395baf495f9559bf5be0 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:19:37 +0200 Subject: [PATCH 10/15] fix: reverting last change --- workflow/rules/preparation.smk | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index b9acbb6..2e634a7 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -197,7 +197,5 @@ rule prepareDocking: path.join(PREPARED_DIR, "receptor", "{receptorID}.pdbqt"), output: path.join(OUTPUT_DIR, "receptor", "{receptorID}.txt"), - run: - import shutil - - shutil.copy(input[0], output[0]) + shell: + "echo {input} > {output}" From ae1409dc5479c24fb6748b25c633ae8eda5727c8 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:42:18 +0200 Subject: [PATCH 11/15] fix: added versioning info --- workflow/envs/basic.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/workflow/envs/basic.yml b/workflow/envs/basic.yml index e69de29..aa65abb 100644 --- a/workflow/envs/basic.yml +++ b/workflow/envs/basic.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - unzip>=6.0 \ No newline at end of file From 0a96d7c22b0f67df3790f6591af43453106da23b Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:42:39 +0200 Subject: [PATCH 12/15] fix: formatting ... again --- workflow/rules/preparation.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 2e634a7..4264075 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -175,7 +175,7 @@ rule prepareGeometry: if len(parts) >= 4: grid_params.append(" ".join(parts[1:4])) - # Reverse the order (equivalent to 'tac') + # Reverse the order (equivalent to 'tac') grid_params.reverse() # Write to output file with space separation and trailing newline From bc5c77399b85225b0cf27198380dfcc83effc8b3 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:46:47 +0200 Subject: [PATCH 13/15] fix: added missing empty line --- workflow/envs/vinalc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/vinalc.yml b/workflow/envs/vinalc.yml index ccd128c..65f2cb2 100644 --- a/workflow/envs/vinalc.yml +++ b/workflow/envs/vinalc.yml @@ -1,4 +1,4 @@ channels: - bioconda dependencies: - - vinalc>=1.4.2 \ No newline at end of file + - vinalc>=1.4.2 From 8322fe0cc3037a40de88f8a84d8ae5d1de6cdf01 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 11:49:29 +0200 Subject: [PATCH 14/15] fix: merge conflict --- workflow/envs/openbabel.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/workflow/envs/openbabel.yml b/workflow/envs/openbabel.yml index 00599ea..7f4d8a8 100644 --- a/workflow/envs/openbabel.yml +++ b/workflow/envs/openbabel.yml @@ -1,10 +1,4 @@ channels: -<<<<<<< HEAD - - conda-forge -dependencies: - - openbabel>=3.1.1 -======= - conda-forge dependencies: - openbabel>=3.1.1 ->>>>>>> main From 60f464b553ccd1cf53848ce83f0aa43140b86a59 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Fri, 10 Oct 2025 12:51:24 +0200 Subject: [PATCH 15/15] fix: enforce formatting --- workflow/envs/basic.yml | 2 +- workflow/rules/preparation.smk | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/envs/basic.yml b/workflow/envs/basic.yml index aa65abb..ca3968b 100644 --- a/workflow/envs/basic.yml +++ b/workflow/envs/basic.yml @@ -1,4 +1,4 @@ channels: - conda-forge dependencies: - - unzip>=6.0 \ No newline at end of file + - gzip>=1.14 diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk index 4264075..c1da5a3 100644 --- a/workflow/rules/preparation.smk +++ b/workflow/rules/preparation.smk @@ -175,7 +175,7 @@ rule prepareGeometry: if len(parts) >= 4: grid_params.append(" ".join(parts[1:4])) - # Reverse the order (equivalent to 'tac') + # Reverse the order (equivalent to 'tac') grid_params.reverse() # Write to output file with space separation and trailing newline