Update rule all

assembly.smk

@@ -107,9 +107,9 @@ def contigs_input(wildcards):
 
 def contigsExpand_input(wildcards):
 	if config["ASSEMBLER"] == "megahit":
-		return [expand("work/megahit/{sample}/{sample}.contigs.fa", sample=SAMPLES)]
+		return [expand("work/megahit/{sample}/{sample}.contigs.fa", sample=config["SAMPLES"])]
 	elif config["ASSEMBLER"] == "metaspades":
-		return [expand("work/metaSPADES/{sample}/{sample}.contigs.fasta", sample=SAMPLES)]
+		return [expand("work/metaSPADES/{sample}/{sample}.contigs.fasta", sample=config["SAMPLES"])]
 
 def coassembly_contigs_input(wildcards):
 	if config["ASSEMBLER"] == "megahit":

count.smk

@@ -15,13 +15,13 @@ rule mapping:
 	input:
 		R1 = "DATA/trim/{reads}_R1.fastq.gz",
 		R2 = "DATA/trim/{reads}_R2.fastq.gz",
-		i = expand("work/index/{{contigs}}.{ext}.bt2l", ext=["1", "2", "3", "4", "rev.1", "rev.2"])
+		i = expand("work/index/{{sample}}.{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-{sample}-{reads}.sam"),
+		bam = "work/bowtie/align-{sample}-{reads}.bam",
+		bai = "work/bowtie/align-{sample}-{reads}.bam.bai"
 	params:
-		index = "work/index/{contigs}"
+		index = "work/index/{sample}"
 	threads:
 		8
 	shell:
@@ -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-{sample}-{reads}.bam",
+		bai = "work/bowtie/align-{sample}-{reads}.bam.bai"
 	output:
-		"report/count-contigs-{contigs}-{reads}.tsv"
+		"report/count-contigs-{sample}-{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-{sample}-{reads}.bam",
+		bai = "work/bowtie/align-{sample}-{reads}.bam.bai"
 	output:
-		"report/count-genes-{contigs}-{reads}.tsv"
+		"report/count-genes-{sample}-{reads}.tsv"
 	shell:
 		"htseq-count "
 		"--format bam "

global.smk

@@ -8,16 +8,18 @@ rule all:
 	input:
 		"report/multiqc_report.html",
 		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
+		#coassembly
 		"report/quast_coassembly/report.html",
 		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
+		expand("report/count-genes-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
+		"report/diamond_nr_coassembly.tsv",
 		"report/contigs_coassembly-taxNames.tsv",
-		expand("report/count-gene-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
 		"report/genes_coassembly-taxNames.tsv",
-		"report/diamond_nr_coassembly.tsv",
-		"work/prokka/coassembly_prokka.tsv",
-		"work/interproscan/coassembly.faa.tsv",
-		"work/cdhit/catalogue.ffn",
+		#catalogue
+		"report/quast_results/report.html",
 		expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),
+		"report/diamond_nr_catalogue.tsv",
+		"report/contigs_catalogue-taxNames.tsv",
 
 
 include: "../workflow_metagenomics/quality.smk"