diff --git a/Snakemake/RNAseqVariantCalling/README.md b/Snakemake/RNAseqVariantCalling/README.md
index 8babe2eec9e9a5668a297967e59943e53681fd75..27d16bff9e2bd381903f5a92b7fa2748b62c92c1 100644
--- a/Snakemake/RNAseqVariantCalling/README.md
+++ b/Snakemake/RNAseqVariantCalling/README.md
@@ -143,7 +143,13 @@ The workflow depends on:
* rsem-calculate-expression ( RSEM version 1.3.0)
* GenomeAnalysisTK.jar (version 3.7)
* java (version 8)
-
+* snakemake (version 4.8.0)
+* maskFastaFromBed (bedtools version 2.26.0)
+* vcf-merge (VCFtools version 0.1.15)
+* bgzip (Tabix version 0.2.5)
+* tabix (Tabix version 0.2.5)
+* python2.7 (version 2.7.2)
+* fastqc (version 0.11.7)
These dependencies are all included in the singularity environment, or must be available in your PATH or in a directory that you must precise in the [config_calling.yaml](example/config_calling.yaml)
diff --git a/Snakemake/RNAseqVariantCalling/Snakefile_calling b/Snakemake/RNAseqVariantCalling/Snakefile_calling
index 785fdf180f1ea2babc8fe2b1a30a55f277be26d6..1270502eb637c4d3f1d7658a33b2b2c617b17ae9 100644
--- a/Snakemake/RNAseqVariantCalling/Snakefile_calling
+++ b/Snakemake/RNAseqVariantCalling/Snakefile_calling
@@ -336,7 +336,7 @@ rule clean_SAM:
jar = config["picard_jar"]
shell:
"""
- java -Xmx{params.mem} -jar {params.jar} CleanSam I = {input.g_bam} O = {output.g_bam}
+ java -Xmx{params.mem} -jar {params.jar} CleanSam I={input.g_bam} O={output.g_bam}
samtools flagstat {output.g_bam} > {output.g_stat}
"""
@@ -450,7 +450,7 @@ def get_RSEM_res(wildcards):
rule merge_rsem:
input:
- count = get_RSEM_res
+ c = get_RSEM_res
output:
out = expand("Results/Summary/{{dir}}_summary_"+POP+"_{{feature}}_{stat}.tsv", stat = STAT)
params:
@@ -503,9 +503,10 @@ rule fai_dict_index:
jar = config["picard_jar"]
shell:
"""
+ mkdir -p Results/Fai_Dict_Index/
ln -s {input.fasta} {output.fasta}
samtools faidx {output.fasta}
- java -Xmx{params.mem} -jar {params.jar} CreateSequenceDictionary R = {output.fasta} O = {output.dict}
+ java -Xmx{params.mem} -jar {params.jar} CreateSequenceDictionary R={output.fasta} O={output.dict}
"""
rule markdup:
diff --git a/Snakemake/RNAseqVariantCalling/example/sample.tsv b/Snakemake/RNAseqVariantCalling/example/sample.tsv
index 4a3fe1435b0984c2d73fbf6c751695b73d6dcf6c..6d2efe1deb5e424300ee574726483007c2a9b15b 100644
--- a/Snakemake/RNAseqVariantCalling/example/sample.tsv
+++ b/Snakemake/RNAseqVariantCalling/example/sample.tsv
@@ -1,3 +1,3 @@
-idx name forward_read reverse_read sequencer read_length oriented phred_scale
+idx sample_name forward_read reverse_read sequencer read_length oriented phred_scale
1 sample_name1 file1_R1.fastq.gz file1_R2.fastq.gz ILLUMINA 100 0.5 64
2 sample_name2 file2.fastq.gz SLX_or_SOLEXA_or_SOLID_or_454_or_LS454_or_COMPLETE_or_PACBIO_or_IONTORRENT_or_CAPILLARY_or_HELICOS_or_UNKNOWN 100 0_or_0.5_or_1 33