From 96ade92b37a12f161317d34fd600033343f97031 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 6 Feb 2026 16:41:21 +0000 Subject: [PATCH 1/6] changing for linting --- workflow/rules/select_best_assembly.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/select_best_assembly.smk b/workflow/rules/select_best_assembly.smk index 361b53f..e6a7fbc 100644 --- a/workflow/rules/select_best_assembly.smk +++ b/workflow/rules/select_best_assembly.smk @@ -13,7 +13,7 @@ rule select_best_assembly: assembly=f"{output_dir}" + "best_assembly/{sample}/{sample}_best_assembly.fa", params: sample="{sample}", - results_dir=output_dir, + results_dir=lambda w, output: os.path.dirname(os.path.dirname(os.path.dirname(output.assembly))) + "/", threads: 1 resources: mem_mb=get_very_low_mem, From 352e34bf1a926b477a365abefbe708e92162bbc9 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 6 Feb 2026 16:44:54 +0000 Subject: [PATCH 2/6] fixing formatting --- workflow/rules/select_best_assembly.smk | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflow/rules/select_best_assembly.smk b/workflow/rules/select_best_assembly.smk index e6a7fbc..be1680e 100644 --- a/workflow/rules/select_best_assembly.smk +++ b/workflow/rules/select_best_assembly.smk @@ -13,7 +13,10 @@ rule select_best_assembly: assembly=f"{output_dir}" + "best_assembly/{sample}/{sample}_best_assembly.fa", params: sample="{sample}", - results_dir=lambda w, output: os.path.dirname(os.path.dirname(os.path.dirname(output.assembly))) + "/", + results_dir=lambda w, output: os.path.dirname( + os.path.dirname(os.path.dirname(output.assembly)) + ) + + "/", threads: 1 resources: mem_mb=get_very_low_mem, From 9d909d565a24f42c51ae0934ddbca47414bf9b8e Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Tue, 10 Feb 2026 15:20:09 +0000 Subject: [PATCH 3/6] rm fastk_merged.smk --- workflow/rules/fastK_merged.smk | 40 --------------------------------- 1 file changed, 40 deletions(-) delete mode 100644 workflow/rules/fastK_merged.smk diff --git a/workflow/rules/fastK_merged.smk b/workflow/rules/fastK_merged.smk deleted file mode 100644 index 454857c..0000000 --- a/workflow/rules/fastK_merged.smk +++ /dev/null @@ -1,40 +0,0 @@ -# This rule generates a FastK table needed to run merquryFK - - -rule fastk_merged: - wildcard_constraints: - reads_type="merged", - input: - merged_in=f"{input_dir}" + "{sample}/{sample}_merge.fq.gz", - output: - ktab=f"{output_dir}" + "{reads_type}/fastk/{sample}/fastk_table.ktab", - hist=f"{output_dir}" + "{reads_type}/fastk/{sample}/fastk_table.hist", - params: - k=config["fastk"]["k"], - result_prefix=lambda wildcards, output: os.path.splitext(output.ktab)[0], - t=config["fastk"]["t"], - memory_gb=lambda wildcards, resources: resources.mem_mb // 1024, - temp_dir=lambda wildcards, output: os.path.join( - os.path.dirname(output.ktab), "temp" - ), - threads: get_low_threads - resources: - mem_mb=get_low_mem, - partition=config["low"]["partition"], - log: - "logs/{sample}/fastk_{reads_type}.log", - benchmark: - "benchmark/{sample}/fastk_{reads_type}.txt" - conda: - "../envs/merquryFK.yaml" - container: - "docker://quay.io/biocontainers/merquryfk:1.1.3--h71df26d_0" - shell: - """ - mkdir -p {params.temp_dir} - - echo "Running FastK with the following command:" >> {log} 2>&1 - echo "FastK -v -T{threads} -k{params.k} -M{params.memory_gb} {input.merged_in} -N{params.result_prefix} -t{params.t} -P{params.temp_dir}" >> {log} 2>&1 - FastK -v -T{threads} -k{params.k} -M{params.memory_gb} {input.merged_in} -N{params.result_prefix} -t{params.t} -P{params.temp_dir} >> {log} 2>&1 - rm -rf {params.temp_dir} # clean up temporary directory - """ From e462b5d807762e4c06b4d2e94c798c6c7e6b7ad9 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Tue, 10 Feb 2026 15:32:00 +0000 Subject: [PATCH 4/6] small update --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index be2e347..eb675c8 100644 --- a/README.md +++ b/README.md @@ -230,7 +230,6 @@ Create `run_snakemake.sh`: #SBATCH --partition=medium #SBATCH --cpus-per-task=4 #SBATCH --mem=8G -#SBATCH --time=48:00:00 #SBATCH --output=snakemake-%j.out #SBATCH --error=snakemake-%j.err From 2d75585c8f5f4a1befe49c50e908e56d94afaa7d Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 13 Feb 2026 09:26:44 +0000 Subject: [PATCH 5/6] output directory set as param not as output --- workflow/rules/select_best_assembly.smk | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/workflow/rules/select_best_assembly.smk b/workflow/rules/select_best_assembly.smk index be1680e..8a09645 100644 --- a/workflow/rules/select_best_assembly.smk +++ b/workflow/rules/select_best_assembly.smk @@ -9,7 +9,6 @@ rule select_best_assembly: ), report=f"{output_dir}" + "quast/{sample}/report.txt", output: - best_assemblies_dir=directory(f"{output_dir}" + "best_assembly/{sample}/"), assembly=f"{output_dir}" + "best_assembly/{sample}/{sample}_best_assembly.fa", params: sample="{sample}", @@ -17,6 +16,8 @@ rule select_best_assembly: os.path.dirname(os.path.dirname(output.assembly)) ) + "/", + best_assemblies_dir=lambda w, output: os.path.dirname(output.assembly) + + "/", threads: 1 resources: mem_mb=get_very_low_mem, @@ -32,6 +33,6 @@ rule select_best_assembly: shell: """ echo "Running the script as follows:" >> {log} 2>&1 - echo "workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {output.best_assemblies_dir}" >> {log} 2>&1 - workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {output.best_assemblies_dir} >> {log} 2>&1 + echo "workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {params.best_assemblies_dir}" >> {log} 2>&1 + workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {params.best_assemblies_dir} >> {log} 2>&1 """ From 5ac71b4bfd998abac1044ea838ff943a4dc5735a Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 13 Feb 2026 09:34:41 +0000 Subject: [PATCH 6/6] formatting --- workflow/rules/select_best_assembly.smk | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/rules/select_best_assembly.smk b/workflow/rules/select_best_assembly.smk index 8a09645..4e5e22d 100644 --- a/workflow/rules/select_best_assembly.smk +++ b/workflow/rules/select_best_assembly.smk @@ -16,8 +16,7 @@ rule select_best_assembly: os.path.dirname(os.path.dirname(output.assembly)) ) + "/", - best_assemblies_dir=lambda w, output: os.path.dirname(output.assembly) - + "/", + best_assemblies_dir=lambda w, output: os.path.dirname(output.assembly) + "/", threads: 1 resources: mem_mb=get_very_low_mem,