Commit 32775673 authored by jacqueslagnel's avatar jacqueslagnel
Browse files

minor

parent a6de1c30
......@@ -21,7 +21,7 @@ rule final_outs:
input:
"{outdir}/multiqc/multiqc_report_fastqc.html".format(outdir=config["outdir"]),
"{outdir}/multiqc/multiqc_report_bam.html".format(outdir=config["outdir"]),
expand("{outdir}/variant/{sample}_freebayes.vcf", outdir=config["outdir"], sample=samples['SampleName'])
"{outdir}/gene_count_dicoexpress.csv".format(outdir=config["outdir"])
#function return only the fastq1 file and adds the fastq path
def get_fastq1(wildcards):
......
#minimal sample file
SampleName fq1 fq2
Montarsa-1107-lot1 25-Montarsa-1107-lot1_CTAGCGCT-GTGTAGAC-AHGL3FDSXX_L002_R1.fastq.gz 25-Montarsa-1107-lot1_CTAGCGCT-GTGTAGAC-AHGL3FDSXX_L002_R2.fastq.gz
Montarsa-2905-lot3 Montarsa-2905-lot3_AACTGTAG-ACGCCGCA-AHGL3FDSXX_L002_R1.fastq.gz Montarsa-2905-lot3_AACTGTAG-ACGCCGCA-AHGL3FDSXX_L002_R2.fastq.gz
sample1 7634_GGACTCCT_L005_R1_002.fastq.gz 7634_GGACTCCT_L005_R2_002.fastq.gz
sample2 Nemared_AGGCAGAA_L005_R1_001.fastq.gz Nemared_AGGCAGAA_L005_R2_001.fastq.gz
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