underscores allowed in sample names

count.smk

@@ -17,9 +17,9 @@ rule mapping:
 		R2 = "DATA/trim/{reads}_R2.fastq.gz",
 		i = expand("work/index/{{contigs}}.{ext}.bt2l", ext=["1", "2", "3", "4", "rev.1", "rev.2"])
 	output:
-		sam = temp("work/bowtie/align_{contigs}_{reads}.sam"),
-		bam = "work/bowtie/align_{contigs}_{reads}.bam",
-		bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
+		sam = temp("work/bowtie/align-{contigs}-{reads}.sam"),
+		bam = "work/bowtie/align-{contigs}-{reads}.bam",
+		bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
 	params:
 		index = "work/index/{contigs}"
 	threads:
@@ -48,10 +48,10 @@ rule mapping:
 
 rule count_contig:
 	input:
-		bam = "work/bowtie/align_{contigs}_{reads}.bam",
-		bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
+		bam = "work/bowtie/align-{contigs}-{reads}.bam",
+		bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
 	output:
-		"report/count-contigs_{contigs}_{reads}.tsv"
+		"report/count-contigs-{contigs}-{reads}.tsv"
 	shell:
 		"samtools idxstats "
 		"{input.bam} "
@@ -61,10 +61,10 @@ rule count_contig:
 rule count_gene:
 	input:
 		unpack(gff_input),
-		bam = "work/bowtie/align_{contigs}_{reads}.bam",
-		bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
+		bam = "work/bowtie/align-{contigs}-{reads}.bam",
+		bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
 	output:
-		"report/count-genes_{contigs}_{reads}.tsv"
+		"report/count-genes-{contigs}-{reads}.tsv"
 	shell:
 		"htseq-count "
 		"--format bam "

global.smk

@@ -9,9 +9,9 @@ rule all:
 		"report/multiqc_report.html",
 		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
 		"report/quast_coassembly/report.html",
-		expand("report/count-contigs_coassembly_{sample}.tsv", sample=config["SAMPLES"]),
+		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
 		"report/contigs_coassembly-taxNames.tsv",
-		expand("report/count-contigs_coassembly_{sample}.tsv", sample=config["SAMPLES"]),
+		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
 		"report/genes_coassembly-taxNames.tsv",
 		"report/diamond_nr_coassembly.tsv",
 		"work/prokka/coassembly_prokka.tsv",