replaced index by name when accessing snakemake variables (issue #29)

rules/Toxin/Combine_Toxin_SignalP.smk

@@ -132,10 +132,10 @@ rule combine_confidence:
     output:
         "{OUTDIR}/{project}/TOXIN/Toxin_prediction/{input_file}_Confidence_HMM_SignalP_ensembled.csv"
     message:
-        "The different confidence files ({input[0]}, {input[1]}, {input[2]}) are combined in a single output file: {output}"
+        "The different confidence files ({input}) are combined in a single output file: {output}"
     params:
         outdir="{OUTDIR}"
     shell:
         """
-        cat {input[0]} {input[1]} {input[2]} | sort > {output}
+        cat {input} | sort > {output}
         """

rules/Toxin/Toxin.smk

@@ -16,7 +16,7 @@ rule run_HMM:
     log:
         "{OUTDIR}/{project}/TOXIN/HMM_toxin/{input_file}/{file_i}.log"
     message:
-        "Run HMM scan on {input[1]} to generate {output}"
+        "Run HMM scan on {input.renamed} to generate {output}"
     params:
         outdir="{OUTDIR}"
     conda:
@@ -25,7 +25,7 @@ rule run_HMM:
         1
     shell:
         """
-        {config[hmmscan_tool]} --cpu {threads} --noali --notextw --tblout {output} {input[0]} {input[1]} &> {log}
+        {config[hmmscan_tool]} --cpu {threads} --noali --notextw --tblout {output} {input.hmm} {input.renamed} &> {log}
         """
 
 # Adjust HMM results to correct format

rules/Toxin/Toxin_report.smk

@@ -21,7 +21,7 @@ rule merge_final:
         outdir="{OUTDIR}"
     shell:
         """
-        join -t $'\\t' <(sort {input[0]}) <(sort {input[1]}) > {output}
+        join -t $'\\t' <(sort {input.translation}) <(sort {input.prediction}) > {output}
         """
 
 rule toxin_report:

rules/Universal/Preprocessing.smk

@@ -38,7 +38,7 @@ rule generate_translation:
         outdir="{OUTDIR}"
     shell:
         """
-        paste {input[0]} {input[1]} | awk 'sub(/^>/,"")' OFS='\\t' > {output}
+        paste {input.renamed} {input.original} | awk 'sub(/^>/,"")' OFS='\\t' > {output}
         """
 
 ###############################

rules/Universal/Preprocessing_contig.smk

@@ -38,5 +38,5 @@ rule generate_ContigTranslation:
         outdir="{OUTDIR}"
     shell:
         """
-        paste {input[0]} {input[1]} | awk 'sub(/^>/,"")' OFS='\\t' > {output}
+        paste {input.renamed} {input.original} | awk 'sub(/^>/,"")' OFS='\\t' > {output}
         """

rules/Virulence/Combine_Virulence_SignalP.smk

@@ -18,7 +18,7 @@ rule merge_SignalPVir:
         "{OUTDIR}/{project}/VIRULENCE/virulence_merged/{input_file}_virulence_SignalP_prediction.tsv"
     shell:
         """
-        join -t $'\\t' <(sort {input[0]}) <(sort {input[1]}) > {output[0]}
+        join -t $'\\t' <(sort {input.Vir}) <(sort {input.SignalP}) > {output}
         """
 
 ###########################################################
@@ -90,4 +90,4 @@ rule SignalVir_virulence_prediction:
     output:
         "{OUTDIR}/{project}/VIRULENCE/Virulence_prediction/{input_file}_Confidence_Virulence_ensembled.csv"
     shell:
-        "cat {input[0]} {input[1]} {input[2]} {input[3]} {input[4]} > {output[0]}"
+        "cat {input} > {output}"

rules/Virulence/Virulence.smk

@@ -16,7 +16,7 @@ rule run_HMM_vir:
     log:
         "{OUTDIR}/{project}/VIRULENCE/HMM_virulence/{input_file}/{file_i}.log"
     message:
-        "Run HMM scan on {input[1]} to generate {output}"
+        "Run HMM scan on {input.renamed} to generate {output}"
     params:
         outdir="{OUTDIR}"
     conda:
@@ -25,7 +25,7 @@ rule run_HMM_vir:
         12
     shell:
         """
-        {config[hmmscan_tool]} --cpu {threads} --noali --notextw --tblout {output} {input[0]} {input[1]} &> {log}
+        {config[hmmscan_tool]} --cpu {threads} --noali --notextw --tblout {output} {input.hmm} {input.renamed} &> {log}
         """
 
 # Adjust HMM results to correct format
@@ -121,7 +121,7 @@ rule HMM_VIR_report:
         temp("{OUTDIR}/{project}/VIRULENCE/HMM_virulence/{input_file}_hmm_prediction_intermediate.tsv")
     shell:
         """
-        cat {input[0]} {input[1]} {input[2]} | sort > {output}
+        cat {input} | sort > {output}
         """
 
 rule HMM_VIR_finalformat:
@@ -222,7 +222,7 @@ rule join_matrix:
                 fi
         }}
 
-        xjoin {input[0]} {input[1]} {input[2]} {input[3]} {input[4]} | sort -k 1n,1 > {output}
+        xjoin {input} | sort -k 1n,1 > {output}
         """
 
 rule classifier:
@@ -277,7 +277,7 @@ rule merge_virulence:
     output:
         "{OUTDIR}/{project}/VIRULENCE/HMM_classifier_virulence/{input_file}_Virulence_prediction.tsv"
     shell:
-        "join -t $'\\t' <(sort {input[0]}) <(sort {input[1]}) > {output};"
+        "join -t $'\\t' <(sort {input.hmm}) <(sort {input.classifier}) > {output};"
         "sed -i $'1 i\\\ ID\\tHMM_prediction\\tmodel_prediction' {output}"
 
 rule virulence_nonpath:
@@ -351,4 +351,4 @@ rule merge_combined:
     output:
         "{OUTDIR}/{project}/VIRULENCE/HMM_classifier_virulence/{input_file}_virulence_final_prediction.tsv"
     shell:
-        "cat {input[0]} {input[1]} {input[2]} {input[3]} {input[4]} {input[5]} > {output}"
+        "cat {input} > {output}"

rules/Virulence/Virulence_report.smk

@@ -22,7 +22,7 @@ rule Virulence_merge_final:
         outdir="{OUTDIR}"
     shell:
         """
-        join -t $'\\t' <(sort {input[0]}) <(sort {input[1]}) > {output}
+        join -t $'\\t' <(sort {input.translation}) <(sort {input.prediction}) > {output}
         """
 
 rule virulence_report:

scripts/AMR_MGE.R

@@ -6,28 +6,28 @@ sink(file=file(snakemake@log[[1]], open="wt"), type="message")
 library(tidyverse)
 
 # AMR prediction
-AMR <- read.delim(file = snakemake@input[[1]], header=FALSE, comment.char="#")
+AMR <- read.delim(file = snakemake@input[["AMR"]], header=FALSE, comment.char="#")
 AMR <- AMR %>% select(1,4,5)
 colnames(AMR) <- c("ARG","GeneID","Category")
 
-AMR_translation<-read.delim(file = snakemake@input[[2]], header=FALSE)
+AMR_translation<-read.delim(file = snakemake@input[["AMR_translation"]], header=FALSE)
 colnames(AMR_translation) <- c("GeneID", "Gene_Name")
 AMR_translation$Gene_Name<- sub('>', '', AMR_translation$Gene_Name)
 
 # Plasmid Prediction
-Plasmid <- read.delim(file = snakemake@input[[3]], header=TRUE)
+Plasmid <- read.delim(file = snakemake@input[["Plasmid"]], header=TRUE)
 Plasmid <- separate(data= Plasmid, col=label, into=c("left", "right"), sep="\\.")
 Plasmid <- Plasmid %>% select(1,2)
 colnames(Plasmid) <-c("ContigID","Plasmid_prediction")
 Plasmid <- Plasmid %>% filter(ContigID != "contig_name")
 Plasmid$ContigID <- sprintf("%010d", Plasmid$ContigID)
 
-Plasmid_translation <- read.delim(file = snakemake@input[[4]], header=FALSE)
+Plasmid_translation <- read.delim(file = snakemake@input[["Contig_translation"]], header=FALSE)
 colnames(Plasmid_translation) <- c("ContigID", "Contig_Name")
 Plasmid_translation$Contig_Name <- sub('>', '', Plasmid_translation$Contig_Name)
 
 # Combine AMR and Plasmid prediction
-Contig_gene_list <- read.delim(file = snakemake@input[[5]], header=FALSE)
+Contig_gene_list <- read.delim(file = snakemake@input[["Contig_gene_list"]], header=FALSE)
 colnames(Contig_gene_list) <- c("Contig_Name", "Gene_Name")
 Contig_gene_list <- merge(Contig_gene_list, AMR_translation, by="Gene_Name", all=TRUE)
 Contig_gene_list <- merge(Contig_gene_list, Plasmid_translation, by="Contig_Name", all=TRUE)
@@ -42,7 +42,7 @@ AMR_Plasmid$Plasmid_prediction <- fct_explicit_na(AMR_Plasmid$Plasmid_prediction
 
 # Phage prediction
 ## VirFinder
-VirFinder <- read.delim(file = snakemake@input[[6]])
+VirFinder <- read.delim(file = snakemake@input[["VirFinder"]])
 VirFinder <- VirFinder %>% select(1,3,4)
 colnames(VirFinder)<- c("ContigID","VirFinder_score","VirFinder_pvalue" )
 VirFinder <- VirFinder %>% filter(ContigID != "name")
@@ -52,7 +52,7 @@ VirFinder$VirFinder_prediction <- ifelse(VirFinder$VirFinder_pvalue <=0.05 & Vir
 VirFinder$ContigID <- sprintf("%010d", VirFinder$ContigID)
 
 ## VirSorter
-vs.pred <- read.csv(file = snakemake@input[[7]], quote="", header=FALSE)
+vs.pred <- read.csv(file = snakemake@input[["VirSorter"]], quote="", header=FALSE)
 vs.head <- setNames(data.frame(matrix(ncol=12, nrow=0)), c("Contig_id","Nb.genes.contigs","Fragment","Nb.genes","Category","Nb.phage.hallmark.genes","Phage.gene.enrichment.sig","Non-Caudovirales.phage.gene.enrichment.sig","Pfam.depletion.sig","Uncharacterized.enrichment.sig","Strand.switch.depletion.sig","Short.genes.enrichment.sig"))
 colnames(vs.pred)<-colnames(vs.head)
 colnames(vs.pred)[1]<- "vs.id"
@@ -84,7 +84,7 @@ AMR_MGE <- AMR_MGE %>% mutate_if(is.factor, fct_explicit_na, na_level = "-")
 AMR_MGE <- AMR_MGE %>% select(2,4,3,5,6,7,10,11)
 AMR_MGE$GeneID <- sprintf("%010d", AMR_MGE$GeneID)
 
-write.csv(AMR_MGE, file=snakemake@output[[1]], row.names=FALSE)
+write.csv(AMR_MGE, file=snakemake@output[["Report_1"]], row.names=FALSE)
 
 AMR_MGE_report <- AMR_MGE
 AMR_MGE_report$origin <- ifelse(AMR_MGE_report$Plasmid_prediction == "chromosome" & AMR_MGE_report$VirFinder_prediction == "-" & AMR_MGE_report$VirSorter_prediction =="-", "chromosome",
@@ -93,6 +93,6 @@ AMR_MGE_report$origin <- ifelse(AMR_MGE_report$Plasmid_prediction == "chromosome
                                               ifelse(AMR_MGE_report$Plasmid_prediction == "unclassified" & AMR_MGE_report$VirFinder_prediction == "-" & AMR_MGE_report$VirSorter_prediction =="-", "unclassified", "ambiguous"))))
 AMR_MGE_report <- AMR_MGE_report %>% select(1,2,3,4,5,9)
 
-write.csv(AMR_MGE_report, file=snakemake@output[[2]], row.names=FALSE)
+write.csv(AMR_MGE_report, file=snakemake@output[["Report_2"]], row.names=FALSE)
 
 

scripts/PathoFact.R

@@ -6,21 +6,21 @@ sink(file=file(snakemake@log[[1]], open="wt"), type="message")
 library(tidyverse)
 
 # load virulence prediction
-Virulence_factors <- read.delim(file=snakemake@input[[1]])
+Virulence_factors <- read.delim(file=snakemake@input[["Virulence_factor"]])
 Virulence_factors <- Virulence_factors %>% select(1,5,7)
 colnames(Virulence_factors) <- c("GeneID","Virulence_factor_prediction","Virulence_confidence_level")
 Virulence_factors$GeneID <- as.numeric(as.character(Virulence_factors$GeneID))
 Virulence_factors$GeneID <- sprintf("%010d", Virulence_factors$GeneID)
 
 # load toxin prediction
-Toxins <- read.delim(file=snakemake@input[[2]])
+Toxins <- read.delim(file=snakemake@input[["Toxins"]])
 Toxins <- Toxins %>% select(1,4,5,6)
 colnames(Toxins) <- c("GeneID","Toxin_prediction", "SignalP", "Toxin_confidence_level")
 Toxins$GeneID <- as.numeric(as.character(Toxins$GeneID))
 Toxins$GeneID <- sprintf("%010d", Toxins$GeneID)
 
 # load AMR prediction
-AMR_MGE <- read.delim(file=snakemake@input[[3]])
+AMR_MGE <- read.delim(file=snakemake@input[["AMR_MGE"]])
 colnames(AMR_MGE) <- c("GeneID","Gene_Name","Contig_Name","ARG_prediction","AMR_Category","MGE_prediction")
 
 # Combine files

scripts/hmm.R

@@ -6,13 +6,13 @@ sink(file=file(snakemake@log[[1]], open="wt"), type="message")
 library(tidyverse)
 library(reshape2)
 
-HMM_results<-read.delim(file = snakemake@input[[1]], header = FALSE)
-ID <- read.delim(file = snakemake@input[[5]], header = FALSE)
+HMM_results<-read.delim(file = snakemake@input[["hmmresults"]], header = FALSE)
+ID <- read.delim(file = snakemake@input[["ID"]], header = FALSE)
 HMM_results<- merge(HMM_results, ID, by.x = "V1", by.y = "V1", all.y = TRUE)
 
-positive <- read.table(file = snakemake@input[[2]], quote="\"", comment.char="")
-negative <- read.table(file = snakemake@input[[3]], quote="\"", comment.char="")
-shared <- read.table(file = snakemake@input[[4]], quote="\"", comment.char="")
+positive <- read.table(file = snakemake@input[["positive"]], quote="\"", comment.char="")
+negative <- read.table(file = snakemake@input[["negative"]], quote="\"", comment.char="")
+shared <- read.table(file = snakemake@input[["shared"]], quote="\"", comment.char="")
 positive$class <- "positive"
 negative$class <- "negative"
 shared$class <- "shared"

scripts/ownHMM_library.R

@@ -9,9 +9,9 @@ sink(file=file(snakemake@log[[1]], open="wt"), type="message")
 ### Input of the different files ###
 ####################################
 
-gene_table_HMM<-read.delim(file = snakemake@input[[1]], comment.char="#")
-translation<-read.delim(file = snakemake@input[[2]], header=FALSE)
-signalP<-read.table(file = snakemake@input[[3]], sep= "\t")
+gene_table_HMM<-read.delim(file = snakemake@input[["input_HMM"]], comment.char="#")
+translation<-read.delim(file = snakemake@input[["translation"]], header=FALSE)
+signalP<-read.table(file = snakemake@input[["signalP"]], sep= "\t")
 
 gene_table_HMM<-gene_table_HMM[,c(1,2,4,3)]
 
@@ -21,7 +21,7 @@ colnames(translation)<-c("ID","Query_sequence")
 translation<-translation[,c(2,1)]
 
 #Description file of the HMM
-library_HMM<-read.table(file = snakemake@input[[4]], sep = ";", header = T, quote = '#')
+library_HMM<-read.table(file = snakemake@input[["library"]], sep = ";", header = T, quote = '#')
 colnames(library_HMM)<-c("HMM_ID","NAME","Alternative_name", "Database", "Description")
 gene_table_library<-merge.data.frame(gene_table_HMM, library_HMM, by.x= "HMM_Name", by.y= "HMM_ID")
 gene_table_library<-gene_table_library[,c(2,1,3,4,5,6,7,8)]
@@ -29,7 +29,7 @@ gene_table_library<-gene_table_library[,c(2,1,3,4,5,6,7,8)]
 gene_table_library<-merge.data.frame(translation, gene_table_library, by.x = "ID", by.y = "Query_sequence")
 gene_table_library$ID<-sprintf("%010d",as.numeric(gene_table_library$ID))
 
-write.csv(gene_table_library,file = snakemake@output[[1]])
+write.csv(gene_table_library,file = snakemake@output[["gene_library"]])
 
 #Toxin/Non-Toxin file
 frequency<-data.frame(table(gene_table_HMM[1]))
@@ -55,4 +55,4 @@ gene_table_Toxic<-as.data.frame(gene_table_Toxic)
 gene_table_Toxic<-merge.data.frame(gene_table_Toxic,signalP,by="Query_sequence")
 gene_table_Toxic$Query_sequence<-sprintf("%010d",as.numeric(gene_table_Toxic$Query_sequence))
 
-write.csv(gene_table_Toxic,file = snakemake@output[[2]])
+write.csv(gene_table_Toxic,file = snakemake@output[["gene_toxic"]])