diff --git a/workflow/rules/01_trycycler_assembly.smk b/workflow/rules/01_trycycler_assembly.smk index f085d2a..660cdab 100644 --- a/workflow/rules/01_trycycler_assembly.smk +++ b/workflow/rules/01_trycycler_assembly.smk @@ -7,7 +7,7 @@ rule clean_nanopore: "../envs/utilities.yaml" threads: 4 log: - "workflow/report/logs/01_trycycler_assembly/{strains}/clean_nanopore-{strains}.log" + "logs/01_trycycler_assembly/{strains}/clean_nanopore-{strains}.log" shell: """ porechop -t {threads} -i {input} -o {output} &>> {log} @@ -21,7 +21,7 @@ rule filter_length: conda: "../envs/utilities.yaml" log: - "workflow/report/logs/01_trycycler_assembly/{strains}/filter_length-{strains}.log" + "logs/01_trycycler_assembly/{strains}/filter_length-{strains}.log" params: min_length = 1000, keep_percent = 95 @@ -37,7 +37,7 @@ rule subsample: temp(expand('data/interim/01_trycycler_assembly/{{strains}}/nanopore/read_subsets/sample_{subsample}.fastq', subsample=['01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12'])) threads: 12 log: - "workflow/report/logs/01_trycycler_assembly/{strains}/subsample-{strains}.log" + "logs/01_trycycler_assembly/{strains}/subsample-{strains}.log" conda: "../envs/trycycler.yaml" params: @@ -57,7 +57,7 @@ rule assemble_flye: graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa', threads: 8 log: - "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_flye/assemble_flye-{strains}_{subsample}.log" + "logs/01_trycycler_assembly/{strains}/assemble_flye/assemble_flye-{strains}_{subsample}.log" wildcard_constraints: subsample="|".join(['01', '04', '07', '10']), conda: @@ -77,7 +77,7 @@ rule assemble_minipolish: graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa' threads: 8 log: - "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_minipolish/assemble_minipolish-{strains}_{subsample}.log" + "logs/01_trycycler_assembly/{strains}/assemble_minipolish/assemble_minipolish-{strains}_{subsample}.log" wildcard_constraints: subsample="|".join(['02', '05', '08', '11']), conda: @@ -112,7 +112,7 @@ rule assemble_raven: graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa' threads: 8 log: - "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_raven/assemble_raven-{strains}_{subsample}.log" + "logs/01_trycycler_assembly/{strains}/assemble_raven/assemble_raven-{strains}_{subsample}.log" wildcard_constraints: subsample="|".join(['03', '06', '09', '12']), conda: @@ -129,7 +129,7 @@ rule draw_graph: graph = temp('data/processed/{strains}/01_trycycler_assembly/{subsample}_{strains}.png'), gfa = 'data/processed/{strains}/01_trycycler_assembly/{strains}_{subsample}.gfa' log: - "workflow/report/logs/01_trycycler_assembly/{strains}/bandage/{strains}_{subsample}.log" + "logs/01_trycycler_assembly/{strains}/bandage/{strains}_{subsample}.log" conda: "../envs/utilities.yaml" shell: @@ -144,7 +144,7 @@ rule merge_draw_graph: output: png = "data/processed/{strains}/01_trycycler_assembly/{strains}_graphs.png", log: - "workflow/report/logs/01_trycycler_assembly/{strains}/bandage/merge_{strains}.log" + "logs/01_trycycler_assembly/{strains}/bandage/merge_{strains}.log" conda: "../envs/utilities.yaml" params: diff --git a/workflow/rules/02_trycycler_cluster.smk b/workflow/rules/02_trycycler_cluster.smk index c19218c..9a0c3d5 100644 --- a/workflow/rules/02_trycycler_cluster.smk +++ b/workflow/rules/02_trycycler_cluster.smk @@ -6,7 +6,7 @@ rule trycycler_cluster: cluster=directory('data/interim/02_trycycler_cluster/{strains}') threads: 12 log: - "workflow/report/logs/02_trycycler_cluster/trycycler_cluster/02_trycycler_cluster-{strains}.log" + "logs/02_trycycler_cluster/trycycler_cluster/02_trycycler_cluster-{strains}.log" conda: "../envs/trycycler.yaml" shell: @@ -20,7 +20,7 @@ rule cluster_dump: output: yaml = 'data/interim/02_trycycler_cluster/cluster.yaml' log: - "workflow/report/logs/02_trycycler_cluster/cluster_dump/cluster_dump.log" + "logs/02_trycycler_cluster/cluster_dump/cluster_dump.log" params: cluster_path = 'data/interim/02_trycycler_cluster' run: @@ -49,7 +49,7 @@ rule cluster_draw: output: png = 'data/processed/{strains}/02_trycycler_cluster/{strains}_cluster.png' log: - "workflow/report/logs/02_trycycler_cluster/cluster_draw/draw_cluster_{strains}.log" + "logs/02_trycycler_cluster/cluster_draw/draw_cluster_{strains}.log" conda: "../envs/R.yaml" shell: diff --git a/workflow/rules/03_trycycler_consensus.smk b/workflow/rules/03_trycycler_consensus.smk index b9abbc9..b930b65 100644 --- a/workflow/rules/03_trycycler_consensus.smk +++ b/workflow/rules/03_trycycler_consensus.smk @@ -5,7 +5,7 @@ rule trycycler_intermediate: reconcile = 'data/interim/03_trycycler_consensus/{strains}/{cluster}_copy.log' threads: 1 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_intermediate/trycycler_intermediate-{cluster}-{strains}.log" + "logs/03_trycycler_consensus/trycycler_intermediate/trycycler_intermediate-{cluster}-{strains}.log" params: cluster_file = config["clusters"] shell: @@ -21,7 +21,7 @@ rule trycycler_reconcile: reconcile = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/2_all_seqs.fasta' threads: 8 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_reconcile/trycycler_reconcile-{cluster}-{strains}.log" + "logs/03_trycycler_consensus/trycycler_reconcile/trycycler_reconcile-{cluster}-{strains}.log" conda: "../envs/trycycler.yaml" params: @@ -39,7 +39,7 @@ rule trycycler_MSA: msa = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/3_msa.fasta' threads: 8 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_MSA/trycycler_MSA-{cluster}-{strains}.log" + "logs/03_trycycler_consensus/trycycler_MSA/trycycler_MSA-{cluster}-{strains}.log" conda: "../envs/trycycler.yaml" params: @@ -58,7 +58,7 @@ rule trycycler_partition: partition = "data/interim/03_trycycler_consensus/{strains}/partition.log" threads: 8 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_partition/trycycler_partition_{strains}.log" + "logs/03_trycycler_consensus/trycycler_partition/trycycler_partition_{strains}.log" conda: "../envs/trycycler.yaml" params: @@ -77,7 +77,7 @@ rule trycycler_consensus: consensus = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/7_final_consensus.fasta' threads: 8 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_consensus/trycycler_consensus-{cluster}-{strains}.log" + "logs/03_trycycler_consensus/trycycler_consensus/trycycler_consensus-{cluster}-{strains}.log" conda: "../envs/trycycler.yaml" shell: @@ -94,7 +94,7 @@ rule medaka_polish: "../envs/trycycler.yaml" threads: 8 log: - "workflow/report/logs/03_trycycler_consensus/medaka_polish/medaka_polish-{cluster}-{strains}.log" + "logs/03_trycycler_consensus/medaka_polish/medaka_polish-{cluster}-{strains}.log" params: model = 'r941_min_sup_g507', cluster = "data/interim/03_trycycler_consensus/{strains}/{cluster}", @@ -112,7 +112,7 @@ rule trycycler_concat: assembly = 'data/interim/03_trycycler_consensus/{strains}/assembly.fasta' threads: 1 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_concat/trycycler_concat-{strains}.log" + "logs/03_trycycler_consensus/trycycler_concat/trycycler_concat-{strains}.log" conda: "../envs/trycycler.yaml" shell: @@ -127,7 +127,7 @@ rule format_final_assembly: assembly = 'data/processed/{strains}/03_trycycler_consensus/{strains}.fna' threads: 1 log: - "workflow/report/logs/03_trycycler_consensus/trycycler_format_final_assembly/trycycler_format_final_assembly-{strains}.log" + "logs/03_trycycler_consensus/trycycler_format_final_assembly/trycycler_format_final_assembly-{strains}.log" conda: "../envs/trycycler.yaml" shell: