adjusted the rules to include mem and runtime for cluster config: updated...

adjusted the rules to include mem and runtime for cluster config: updated configs; added slurm config; added cluster scripts; other minor updates

README.md

@@ -82,7 +82,7 @@ Each sample should have three input files:
     - contig and gene IDs should be the same as in the FASTA files
 
 The files should be located in the same directory.
-For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna`, `SAMPLE_A.fna` and `SAMPLE_A.contig` for sample `SAMPLE_A`.
+For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna`, `SAMPLE_A.faa` and `SAMPLE_A.contig` for sample `SAMPLE_A`.
 
 **NOTE**: For preprocessing and assembly of metagenomic reads we would suggest using IMP (https://imp.pages.uni.lu/web/)
 
@@ -92,9 +92,9 @@ For each sample, the corresponding input files should have the same basename, e.
 
 To run PathoFact you need to adjust some parameters in `config.yaml`.
 
-- `input_file`: This is a list of sample names, e.g. `input_file: ["SAMPLE_A","SAMPLE_B"]`
-- `project`: A unique project name which will be used as the name of the output directory in `OUTDIR` path (see below).
-- `OUTDIR`: Path to directory containing the sample data; the output directory will be created there.
+- `sample`: This is a list of sample names, e.g. `sample: ["SAMPLE_A","SAMPLE_B"]`
+- `project`: A unique project name which will be used as the name of the output directory in `datapath` path (see below).
+- `datapath`: Path to directory containing the sample data; the output directory will be created there.
 - `workflow`: Pathofact can run the complete pipeline (default) or a specific step:
     - "complete": complete pipeline = toxin + virulence + AMR + MGE prediction
     - "Tox": toxin prediction
@@ -120,3 +120,12 @@ snakemake -s Snakefile --use-conda --reason --cores <cores> -p
 **NOTE**: It is advised to run the pipeline using multiple CPUs or CPUs with "higher" memory.
 
 For more options, see the [snakemake documentation](https://snakemake.readthedocs.io/en/stable/index.html).
+
+### Execution on a cluster
+
+The pipeline can be run on a cluster using `slurm`.
+The command can be found in the script `cluster.sh` which can also be used to submit the jobs to the cluster.
+
+```bash
+sbatch cluster.sh
+```

Snakefile

@@ -2,51 +2,51 @@
 
 configfile: "config.yaml"
 
-if config["workflow"] == "complete":
+if config["pathofact"]["workflow"] == "complete":
     include:
         "workflows/Combine_PathoFact_workflow.smk"
     rule all:
         input:
             expand(
                 [
-                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
-                    "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
-                    "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
+                    "{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv",
+                    "{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
+                    "{datadir}/{project}/PathoFact_{sample}_predictions.csv"
                 ],
-                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+                datadir=config["pathofact"]["datadir"], project=config["pathofact"]["project"], sample=config["pathofact"]["sample"]
             )
-elif config["workflow"] == "Tox":
+elif config["pathofact"]["workflow"] == "Tox":
     include:
         "workflows/Toxin_workflow.smk"
     rule all:
         input:
             expand(
                 [
-                    "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
-                    "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"
+                    "{datadir}/{project}/Toxin_prediction_{sample}_report.csv",
+                    "{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv"
                 ],
-                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+                datadir=config["pathofact"]["datadir"], project=config["pathofact"]["project"], sample=config["pathofact"]["sample"]
             )
-elif config["workflow"] == "Vir":
+elif config["pathofact"]["workflow"] == "Vir":
     include:
         "workflows/Virulence_workflow.smk"
     rule all:
         input:
             expand(
-                "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
-                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+                "{datadir}/{project}/Virulence_prediction_{sample}_report.csv",
+                datadir=config["pathofact"]["datadir"], project=config["pathofact"]["project"], sample=config["pathofact"]["sample"]
             )                    
-elif config["workflow"] == "AMR":
+elif config["pathofact"]["workflow"] == "AMR":
     include:
         "workflows/AMR_workflow.smk"
     rule all:
         input:
             expand(
                 [
-                    "{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
-                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
+                    "{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv",
+                    "{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv"
                 ],
-                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
+                datadir=config["pathofact"]["datadir"], project=config["pathofact"]["project"], sample=config["pathofact"]["sample"]
             )
 else:
-    raise Exception("Unknown workflow option: %s" % config["workflow"])
+    raise Exception("Unknown workflow option: %s" % config["pathofact"]["workflow"])

cluster.sh

+#!/bin/bash -l
+
+#SBATCH -J PathoFact
+#SBATCH -N 1
+#SBATCH -n 1
+#SBATCH -c 1
+#SBATCH --time=0-6:00:00
+#SBATCH -p batch
+#SBATCH --qos=qos-batch
+
+# activate env
+conda activate PathoFact
+
+# run pipeline
+snakemake -s Snakefile --configfile config.yaml \
+--use-conda --cores 10 --reason -p \
+--cluster-config cluster.yaml --cluster \
+"{cluster.call} {cluster.partition} {cluster.quality} {cluster.nodes} \
+{cluster.runtime}{params.runtime} {cluster.mem_per_cpu}{params.mem} \
+{cluster.threads}{threads} {cluster.job-name} {cluster.output}"

cluster.yaml

+__default__:
+  call: "sbatch"
+  nodes: ""
+  mem_per_cpu: "--mem-per-cpu " # in rule params
+  partition: "-p batch"
+  quality: "-q qos-batch"
+  runtime: "-t" # in rule params
+  threads: "-n"
+  job-name: "-J PathoFact.{rule}"
+  output: "-o slurm-%j.%N-%x.out"
+
+run_PLASMID:
+  nodes: "-N 1"
+  partition: "-p bigmem"
+  quality: "-q qos-bigmem"
+
+run_VirSorter:
+  nodes: "-N 1"
+  partition: "-p bigmem"
+  quality: "-q qos-bigmem"
+
+run_VirFinder:
+  nodes: "-N 1"
+  partition: "-p bigmem"
+  quality: "-q qos-bigmem"

config.yaml

-# Insert name of input files to run analysis
-# All three input files used by the pipeline for one sample need to be given the same name, followed by the suffix .faa (amino acid, gene fasta file), .fna (nucleotide contig fasta file), .contig (table with contig and gene names).
-# Only give name of files and not the suffix (.faa, .fna, .contig)
-input_file: ["SAMPLE_A","SAMPLE_B"]
-
-# Define unique name for your project
-project: Project_A_PathoFact
-
-# Define dir to files (wil also be the output directory
-OUTDIR: /path/to/samples
-
-# Define size of split fasta files (default 10 000 sequences/file)
-size_fasta: 100000
-
-# Workflow (default: "complete")
-# complete: complete pipeline: Tox + Vir + AMR prediction
-# Tox:      toxin prediction
-# Vir:      virulence prediction
-# AMR:      antimicrobial resistance (AMR) & mobile genetic element (MGE) prediction
-workflow: "complete"
-
-###########    
-# SignalP #
-###########
- 
-# Define path to signalP
-signalp: "/path/to/signalp-4.1/signalp"
-
-############
-#   Toxin  #
-############
-
-# Define path to HMM
-hmmscan_tool: "hmmsearch"
-hmm_file: "databases/toxins/combined_Toxin.hmm"
-
-#################
-#    Virulence  #
-#################
-
-vir_hmm_file: "databases/virulence/Virulence_factor.hmm"
-
-#############
-#    AMR    #
-#############
-# Define path to deepARG
-deep_ARG: "submodules/deeparg-ss/deepARG.py"
-
-#Define path to Plasflow
-Plasflow: "PlasFlow.py"
-
-# Define path to phage prediction tools
-# Virsorter
-virsorter: "wrapper_phage_contigs_sorter_iPlant.pl"
-virsorter_data: "scripts/virsorter-data"
-
-#VirFinder
-DeepVirFinder: "submodules/DeepVirFinder/dvf.py"
+pathofact:
+  sample: ["SAMPLE_A","SAMPLE_B"] # requires user input
+  project: Project_A_PathoFact # requires user input
+  datadir: /path/to/samples # requires user input
+  workflow: "complete"
+  size_fasta: 10000
+  scripts: "scripts"
+  signalp: "/path/to/signalp-4.1/signalp" # requires user input
+  deeparg: "submodules/deeparg-ss/deepARG.py"
+  deepvirfinder: "submodules/DeepVirFinder/dvf.py"
+  tox_hmm: "databases/toxins/combined_Toxin.hmm"
+  tox_lib: "databases/library_HMM_Toxins.csv"
+  vir_hmm: "databases/virulence/Virulence_factor.hmm"
+  vir_domains: "databases/models_and_domains"
+  plasflow_threshold: 0.7
+  plasflow_minlen: 1000
+  runtime:
+    short: "00:10:00"
+    medium: "01:00:00"
+    long: "02:00:00"
+  mem:
+    normal_mem_per_core_gb: "4G"
+    big_mem_cores: 4
+    big_mem_per_core_gb: "30G"

rules/AMR/AMR.smk

@@ -3,34 +3,33 @@
 import glob
 import os
 
-PROJECT = config["project"]
-INPUT   = config["input_file"]
-
 ##########################
 #     AMR Prediction     #
 ##########################
 
 rule run_deepARG:
     input:
-        "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
+        "{datadir}/{project}/splitted/{sample}/{file_i}.faa"
     output:
-        temp("{OUTDIR}/{project}/AMR/deepARG_results/{input_file}/{file_i}.out.mapping.ARG")
+        temp("{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG")
     log:
-        "{OUTDIR}/{project}/AMR/deepARG_results/{input_file}/{file_i}.out.mapping.ARG.log"
+        "{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["medium"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     conda:
         "../../envs/DeepARG.yaml"
     shell:
-        "python {config[deep_ARG]} --align --type prot --genes --input {input} --output {wildcards.OUTDIR}/{wildcards.project}/AMR/deepARG_results/{wildcards.input_file}/{wildcards.file_i}.out &> {log}"
+        "python {config[pathofact][deeparg]} --align --type prot --genes --input {input} --output {wildcards.datadir}/{wildcards.project}/AMR/deepARG_results/{wildcards.sample}/{wildcards.file_i}.out &> {log}"
 
 def aggregate_AMR(wildcards):
     checkpoint_output = checkpoints.splitting.get(**wildcards).output.splits
     return expand(
-        "{OUTDIR}/{project}/AMR/deepARG_results/{input_file}/{file_i}.out.mapping.ARG",
-        OUTDIR=wildcards.OUTDIR,
+        "{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG",
+        datadir=wildcards.datadir,
         project=wildcards.project,
-        input_file=wildcards.input_file,
+        sample=wildcards.sample,
         file_i=glob_wildcards(os.path.join(checkpoint_output, "{i}.faa")).i
     )
 
@@ -38,8 +37,10 @@ rule aggregate_deepARG:
     input:
         aggregate_AMR
     output:
-        "{OUTDIR}/{project}/AMR/deepARG_results/{input_file}.out.mapping.ARG"
+        "{datadir}/{project}/AMR/deepARG_results/{sample}.out.mapping.ARG"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         "cat {input} > {output}"

rules/AMR/Combine_MGE_AMR.smk

@@ -3,29 +3,28 @@
 import glob
 import os
 
-PROJECT = config["project"]
-INPUT   = config["input_file"]
-
 ##########################
 #     AMR Prediction     #
 ##########################
 
 rule combine_AMR_plasmid:
     input:
-        AMR="{OUTDIR}/{project}/AMR/deepARG_results/{input_file}.out.mapping.ARG",
-        AMR_translation="{OUTDIR}/{project}/renamed/{input_file}_translation.tsv",
-        Plasmid="{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv",
-        Contig_translation="{OUTDIR}/{project}/renamed/{input_file}_Contig_translation.tsv",
-        Contig_gene_list="{OUTDIR}/{input_file}.contig",
-        VirFinder="{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
-        VirSorter="{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv"
+        AMR="{datadir}/{project}/AMR/deepARG_results/{sample}.out.mapping.ARG",
+        AMR_translation="{datadir}/{project}/renamed/{sample}_translation.tsv",
+        Plasmid="{datadir}/{project}/MGE/plasmid/{sample}_plasflow_prediction_final.tsv",
+        Contig_translation="{datadir}/{project}/renamed/{sample}_Contig_translation.tsv",
+        Contig_gene_list="{datadir}/{sample}.contig",
+        VirFinder="{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv",
+        VirSorter="{datadir}/{project}/MGE/phage/{sample}_VIRSorter_aggregated.csv"
     output:    
-        Report_1=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.csv"),
-        Report_2=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_report_temp.csv")
+        Report_1=temp("{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_detail_temp.csv"),
+        Report_2=temp("{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_report_temp.csv")
     log:
-        "{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.log"
+        "{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_detail_temp.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["medium"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     conda:
         "../../envs/R.yaml"
     script:
@@ -33,11 +32,13 @@ rule combine_AMR_plasmid:
 
 rule modify_details:
     input:
-        "{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.csv"
+        "{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_detail_temp.csv"
     output:
-        "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
+        "{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         """
         sed 's/"//g' {input} | sed 's/,/\\t/g' > {output}
@@ -45,11 +46,13 @@ rule modify_details:
 
 rule modify_report:
     input:
-        "{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_report_temp.csv"
+        "{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_report_temp.csv"
     output:
-        "{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv"
+        "{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         """
         sed 's/"//g' {input} | sed 's/,/\\t/g' > {output}

rules/AMR/Phage.smk

@@ -3,9 +3,6 @@
 import glob
 import os
 
-PROJECT = config["project"]
-INPUT   = config["input_file"]
-
 ##########################
 #     Phage Prediction   #
 ##########################
@@ -14,81 +11,91 @@ INPUT   = config["input_file"]
 
 checkpoint splitphage:
     input:
-        "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
+        "{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
     output:
-        split=directory("{OUTDIR}/{project}/contig_splitted/{input_file}/")
+        split=directory("{datadir}/{project}/contig_splitted/{sample}/")
     log:
-        "{OUTDIR}/{project}/contig_splitted/{input_file}.log"
+        "{datadir}/{project}/contig_splitted/{sample}.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["medium"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
+        split=config["pathofact"]["size_fasta"]
     conda:
         "../../envs/SeqKit.yaml"
     shell:
         """
-        seqkit split2 -s 10000 {input} -O {wildcards.OUTDIR}/{wildcards.project}/contig_splitted/{wildcards.input_file} &> {log}
+        seqkit split2 -s {params.split} {input} -O {wildcards.datadir}/{wildcards.project}/contig_splitted/{wildcards.sample} &> {log}
         """
 
 rule run_VirSorter:
     input:
-        "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
+        "{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
     output:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virsorter/VIRSorter_global-phage-signal.csv"
+        "{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.csv"
     log:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virsorter/VIRSorter_global-phage-signal.log"
+        "{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["long"],
+        mem=config["pathofact"]["mem"]["big_mem_per_core_gb"]
     conda:
         "../../envs/VirSorter.yaml"
     threads:
-        12
+        config["pathofact"]["mem"]["big_mem_cores"]
     shell:
         """
-        {config[virsorter]} -f {input} --ncpu {threads} --wdir {wildcards.OUTDIR}/{wildcards.project}/MGE/phage/{wildcards.input_file}/virsorter --data-dir {config[virsorter_data]} &> {log}
+        wrapper_phage_contigs_sorter_iPlant.pl -f {input} --ncpu {threads} --wdir {wildcards.datadir}/{wildcards.project}/MGE/phage/{wildcards.sample}/virsorter --data-dir {config[pathofact][scripts]}/virsorter-data &> {log}
         """
 
-rule aggregate_Virsorter:
+localrules: aggregate_VirSorter
+rule aggregate_VirSorter:
     input:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virsorter/VIRSorter_global-phage-signal.csv"
+        "{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.csv"
     output:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv"
+        "{datadir}/{project}/MGE/phage/{sample}_VIRSorter_aggregated.csv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}"
     shell:
         "mv {input} {output}"
 
 # VIRFINDER Prediction
-rule run_Virfinder:
+rule run_VirFinder:
     input:
-        "{OUTDIR}/{project}/contig_splitted/{input_file}/{file_i}.fna"
+        "{datadir}/{project}/contig_splitted/{sample}/{file_i}.fna"
     output:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt"
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt"
     log:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virfinder/{file_i}.fna_gt1bp_dvfpred.log"
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["long"],
+        mem=config["pathofact"]["mem"]["big_mem_per_core_gb"]
     conda:
         "../../envs/DeepVirFinder.yaml"
     threads:
-        12
+        config["pathofact"]["mem"]["big_mem_cores"]
     shell:
-        "python {config[DeepVirFinder]} -i {input} -o {wildcards.OUTDIR}/{wildcards.project}/MGE/phage/{wildcards.input_file}/virfinder -c {threads} &> {log}"
+        "python {config[pathofact][deepvirfinder]} -i {input} -o {wildcards.datadir}/{wildcards.project}/MGE/phage/{wildcards.sample}/virfinder -c {threads} &> {log}"
 
-def aggregate_virfinder(wildcards):
+def aggregate_VirFinder(wildcards):
     checkpoint_output= checkpoints.splitphage.get(**wildcards).output.split
     return expand(
-        "{OUTDIR}/{project}/MGE/phage/{input_file}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt",
-        OUTDIR=wildcards.OUTDIR,
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt",
+        datadir=wildcards.datadir,
         project=wildcards.project,
-        input_file=wildcards.input_file,
+        sample=wildcards.sample,
         file_i=glob_wildcards(os.path.join(checkpoint_output, "{i}.fna")).i
     )
 
-rule aggregate_Virfinder:
+rule aggregate_VirFinder:
     input:
-        aggregate_virfinder
+        aggregate_VirFinder
     output:
-        "{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv"
+        "{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         "cat {input} >{output}"

rules/AMR/Plasmid.smk

@@ -3,9 +3,6 @@
 import glob
 import os
 
-PROJECT = config["project"]
-INPUT   = config["input_file"]
-
 ##########################
 #   Plasmid Prediction   #
 ##########################
@@ -13,58 +10,67 @@ INPUT   = config["input_file"]
 # PlasFlow Preprocessing
 rule filter_seq:
     input:
-        "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
+        "{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
     output:
-        "{OUTDIR}/{project}/{input_file}_filtered.fna"
+        "{datadir}/{project}/{sample}_filtered.fna"
     log:
-        "{OUTDIR}/{project}/{input_file}_filtered.log"
+        "{datadir}/{project}/{sample}_filtered.log"
     conda:
         "../../envs/Biopython.yaml"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["medium"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
+        minlen=config["pathofact"]["plasflow_minlen"]
     shell:
-        "./scripts/filter.pl 1000 {input} > {output} 2> {log}"
+        "{config[pathofact][scripts]}/filter.pl {params.minlen} {input} > {output} 2> {log}"
 
 checkpoint splitplasmid:
     input:
-        "{OUTDIR}/{project}/{input_file}_filtered.fna"
+        "{datadir}/{project}/{sample}_filtered.fna"
     output:
-        split=directory("{OUTDIR}/{project}/MGE/plasmid_splitted/{input_file}/")
+        split=directory("{datadir}/{project}/MGE/plasmid_splitted/{sample}/")
     log:
-        "{OUTDIR}/{project}/MGE/plasmid_splitted/{input_file}.log"
+        "{datadir}/{project}/MGE/plasmid_splitted/{sample}.log"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["medium"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
+        split=config["pathofact"]["size_fasta"]
     conda:
         "../../envs/SeqKit.yaml"
     shell:
         """
-        seqkit split2 -s 10000 {input} -O {wildcards.OUTDIR}/{wildcards.project}/MGE/plasmid_splitted/{wildcards.input_file} &> {log}
+        seqkit split2 -s {params.split} {input} -O {wildcards.datadir}/{wildcards.project}/MGE/plasmid_splitted/{wildcards.sample} &> {log}
         """
 
 # PlasFlow Plasmid prediction
 rule run_PLASMID:
     input:
-        "{OUTDIR}/{project}/MGE/plasmid_splitted/{input_file}/{file_i}.fna"
+        "{datadir}/{project}/MGE/plasmid_splitted/{sample}/{file_i}.fna"
     output:
-        temp("{OUTDIR}/{project}/MGE/plasmid/{input_file}/{file_i}_plasflow_prediction.tsv")
+        temp("{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.tsv")
     log:
-        "{OUTDIR}/{project}/MGE/plasmid/{input_file}/{file_i}_plasflow_prediction.log"
+        "{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.log"
     conda:
         "../../envs/PlasFlow.yaml"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["long"],
+        mem=config["pathofact"]["mem"]["big_mem_per_core_gb"],
+        threshold=config["pathofact"]["plasflow_threshold"]
     shell:
         """
-        {config[Plasflow]} --input {input} --output {output} --threshold 0.7 &> {log}
+        PlasFlow.py --input {input} --output {output} --threshold {params.threshold} &> {log}
         """
 
 def aggregate_plasmid_input(wildcards):
     checkpoint_output= checkpoints.splitplasmid.get(**wildcards).output.split
     return expand(
-        "{OUTDIR}/{project}/MGE/plasmid/{input_file}/{file_i}_plasflow_prediction.tsv",
-        OUTDIR=wildcards.OUTDIR,
+        "{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.tsv",
+        datadir=wildcards.datadir,
         project=wildcards.project,
-        input_file=wildcards.input_file,
+        sample=wildcards.sample,
         file_i=glob_wildcards(os.path.join(checkpoint_output, "{i}.fna")).i
     )
 
@@ -72,19 +78,23 @@ rule Plasmid_aggregate:
     input:
         aggregate_plasmid_input
     output:
-        "{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_aggregated.tsv"
+        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_aggregated.tsv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         "cat {input} > {output}"
 
 rule select:
     input:
-        "{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_aggregated.tsv"
+        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_aggregated.tsv"
     output:
-        "{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv"
+        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_prediction_final.tsv"
     params:
-        outdir="{OUTDIR}"
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
     shell:
         """
         cut -f 3,6 {input} > {output}

rules/Toxin/Combine_Toxin_SignalP.smk

@@ -3,9 +3,6 @@
 import glob
 import os
 
-PROJECT = config["project"]
-INPUT   = config["input_file"]
-
 #################################
 # Combine Toxin HMM and SignalP #
 #################################
@@ -13,19 +10,21 @@ INPUT   = config["input_file"]
 # Put Toxin HMM results in the correct format & join SignalP and Toxin HMM files
 rule R_script:
     input:
-        input_HMM="{OUTDIR}/{project}/TOXIN/HMM_toxin/{input_file}.Input_HMM_R.csv",
-        translation="{OUTDIR}/{project}/renamed/{input_file}_translation.tsv",