Commit 64f16ef6 authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

add a new conda environment for fastqc execution - change encoding to C.UTF-8 for multiqc execution

parent 0a9e267f
2834d3e3f6c4e0c2019ac21daae64906 Results/Samples/80_CT_1_chr22/STAR/80_CT_1_chr22Aligned.sortedByCoord.out.bam.bai
c48ad08ad56da40edb9b83b62bbc7866 Results/Samples/81_CT_2_chr22/STAR/81_CT_2_chr22Aligned.sortedByCoord.out.bam.bai
d8fcfe4ecd2296bb6406a9eb980e63ad Results/Samples/82_CT_3_chr22/STAR/82_CT_3_chr22Aligned.sortedByCoord.out.bam.bai
8a3d3b07996ff873812c97415ac0b403 Results/Samples/83_CT_4_chr22/STAR/83_CT_4_chr22Aligned.sortedByCoord.out.bam.bai
1e4523f096481fbed2d9e40e0234076f Results/Samples/96_BEZ_1_chr22/STAR/96_BEZ_1_chr22Aligned.sortedByCoord.out.bam.bai
8a8dc92c964353408b62be4084b5f85b Results/Samples/97_BEZ_2_chr22/STAR/97_BEZ_2_chr22Aligned.sortedByCoord.out.bam.bai
d366f1f9352aee8a656cdd2cddbf7e72 Results/Samples/98_BEZ_3_chr22/STAR/98_BEZ_3_chr22Aligned.sortedByCoord.out.bam.bai
494026c67a30d0a74e310df2177d2d2c Results/Samples/99_BEZ_4_chr22/STAR/99_BEZ_4_chr22Aligned.sortedByCoord.out.bam.bai
188cef50a5571c7be02cd2ca6bc95079 Results/Samples/80_CT_1_chr22/STAR/80_CT_1_chr22Aligned.sortedByCoord.out.bam.bai
5cb69db524161a575ac3311ff7a2bb70 Results/Samples/81_CT_2_chr22/STAR/81_CT_2_chr22Aligned.sortedByCoord.out.bam.bai
11a724beeb315d4d08ecdb7b419fa273 Results/Samples/82_CT_3_chr22/STAR/82_CT_3_chr22Aligned.sortedByCoord.out.bam.bai
201706cef660f7d6dc37d36eb54d7dcb Results/Samples/83_CT_4_chr22/STAR/83_CT_4_chr22Aligned.sortedByCoord.out.bam.bai
20028f297d8cc6e0cce2583cb2f0b94f Results/Samples/96_BEZ_1_chr22/STAR/96_BEZ_1_chr22Aligned.sortedByCoord.out.bam.bai
5c6db45c77403f91134e8094b0b84d5b Results/Samples/97_BEZ_2_chr22/STAR/97_BEZ_2_chr22Aligned.sortedByCoord.out.bam.bai
dd8ff851b67f3f06cdf6046f173e8c3a Results/Samples/98_BEZ_3_chr22/STAR/98_BEZ_3_chr22Aligned.sortedByCoord.out.bam.bai
2b66d79098e4541950d940d12b066b88 Results/Samples/99_BEZ_4_chr22/STAR/99_BEZ_4_chr22Aligned.sortedByCoord.out.bam.bai
......@@ -7,8 +7,10 @@ echo "SNAKEMAKE_JOBS=$2"
export PATH=${1}/miniconda/bin:$PATH
echo $PATH
export LC_ALL=en_US.utf8
export LANG=en_US.utf-8
#export LC_ALL=en_US.utf8
#export LANG=en_US.utf-8
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
# Creation of a conda virtual environment
echo "=== create a conda environment ==="
......
......@@ -117,7 +117,7 @@ rule all:
rule fastqc:
input: OUTPUTDIR+"/Samples/{sampleName}/FASTQC/{sampleName}_{read}.fastq.gz"
output: OUTPUTDIR+"/Samples/{sampleName}/FASTQC/{sampleName}_{read}_fastqc.html"
conda: "CONDA/rnaSeqQuantif.yml"
conda: "CONDA/fastQC.yml"
shell: "fastqc -o " + OUTPUTDIR+"/Samples/{wildcards.sampleName}/FASTQC/ {input}"
rule concat_fastq_chunks:
......
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