fix bugs

Includes/Quantification_Ref.snake

@@ -11,11 +11,11 @@ rule featureCounts:
 
 rule merge_featureCounts:
     input:
-        readscounts = expand(config["Quantification_Dir"] + "/{sample}.readscount", sample = SAMPLES)
+        readscounts = expand(config["Quantification_Dir"] + "/{sample}.count", sample = SAMPLES)
     output:
         gene_expr_matrix = config["Quantification_Dir"] + "/my.gene.TMM.EXPR.matrix",
         gene_counts_matrix = config["Quantification_Dir"] + "/my.gene.counts.matrix"
     shell:
         "perl script/abundance_estimates_to_matrix.pl --est_method featureCounts"
         " --out_prefix " + config["Quantification_Dir"] + "/my.gene"
-        " {input.counts};"
+        " {input.readscounts};"

Snakefile.test

@@ -1,62 +0,0 @@
-import pandas as pd
-
-######################################################
-# read samples.txt to dict
-######################################################
-SAMPLES = pd.read_csv('samples.txt', header=None, sep="\t").set_index(1, drop=False)[0].to_dict()
-
-
-######################################################
-# rules
-######################################################
-rule all:
-    input:
-        "Quantification/my.gene.counts.matrix",             										# gene counts matrix
-        "Quantification/my.gene.TMM.EXPR.matrix",           										# TMP and TMM normalized matrix
-rule hisat2_build:
-    input:
-        genome = "ref/genome.fasta"
-    output:
-        expand("ref/genome.fasta.{index}.ht2", index = range(1,9))
-    log:
-        "Mapping/hisat2-build.log"
-    shell:
-        "hisat2-build {input.genome} {input.genome} 1>{log} 2>&1"
-
-rule hisat2:
-    input:
-        expand("ref/genome.fasta.{index}.ht2", index = range(1,9)),
-        left = "Data/{sample}_1.fq.gz",
-        right = "Data/{sample}_2.fq.gz"
-    output:
-        bam = "Mapping/{sample}.bam"
-    threads: 6
-    log: "Mapping/{sample}.log"
-    shell:
-        "hisat2 --new-summary -p {threads} -x ref/genome.fasta" 
-        " -1 {input.left} -2 {input.right}"
-        " 2>{log} | "
-        " samtools view -Sb - | "
-        " samtools sort -o {output.bam} -" 
-
-rule featureCounts:
-    input:
-        bam = "Mapping/{sample}.bam",
-        gtf = "ref/genome.gtf"
-    output:
-        count = "Quantification/{sample}.count"
-    threads: 6
-    shell:
-        "Rscript script/run-featurecounts.R -b {input.bam} -g {input.gtf} -o " +
-        "Quantification/{wildcards.sample}"
-
-rule merge_featureCounts:
-    input:
-        counts = expand("Quantification/{sample}.count", sample = ['Col-0-0h-rep1', 'Col-0-0h-rep2', 'Col-0-24h-rep1', 'Col-0-24h-rep2'])
-    output:
-        gene_expr_matrix = "Quantification/my.gene.TMM.EXPR.matrix",
-        gene_counts_matrix = "Quantification/my.gene.counts.matrix"
-    shell:
-        "perl script/abundance_estimates_to_matrix.pl --est_method featureCounts"
-        " --out_prefix Quantification/my.gene"
-        " {input.counts};"