Commit 0187c2d5 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

changed to work

parent f5af899d
# path or URL to sample sheet (TSV format(tab , no quote), columns: SampleName fq1 fq2 ...)
samplesfile : "Reads_melo_chinois_epgv.csv"
fq_dir : "/work2/project/redd_vat_phyton/DurArmel/reads_melo_chinois"
outdir : "/work2/project/redd_vat_phyton/DurArmel/analysis_payzawat/out"
fq_dir : "/work/project/redd_vat_phyton/DurArmel/reads_melo_chinois"
outdir : "/work/project/redd_vat_phyton/DurArmel/analysis_payzawat/out"
GENOME : "GCA_009760825.1_ASM976082v1_genomic_chr0_chr12.fasta"
GENOME_FAI : "GCA_009760825.1_ASM976082v1_genomic_chr0_chr12.fasta.fai"
REFPATH : "/work2/project/redd_vat_phyton/DurArmel/analysis_payzawat/ref_payzawat"
REFPATH : "/work/project/redd_vat_phyton/DurArmel/analysis_payzawat/ref_payzawat"
# adapter in fasta 4 cutadapt if used
cutadapt_adapters : "cutadapt_adapters.fas"
......@@ -53,15 +53,15 @@ indel_ReadPosRankSum_filter : "< -20.0"
# ---------------------- singularity config -----------------------------
# singularity images location
fastqc_bin : "/work2/project/gafl/tools/containers/fastqc_V0.11.8.sif"
multiqc_bin : "/work2/project/gafl/tools/containers/multiqc_v1.7.sif"
cutadapt_bin : "/work2/project/gafl/tools/containers/cutadapt_v2.7.sif"
fastp_bin : "/work2/project/gafl/tools/containers/fastp_0.20.0.sif"
samtools_bin : "/work2/project/gafl/tools/containers/samtools_v1.9.sif"
bwa_bin : "/work2/project/gafl/tools/containers/bwa_0.7.17.sif"
sambamba_bin : "/work2/project/gafl/tools/containers/sambamba_v0.7.1.sif"
gatk4_bin : "/work2/project/gafl/tools/containers/gatk4_v4.1.4.1.sif"
R_bin : "/work2/project/gafl/tools/containers/R_base_V3.6.0.sif"
fastqc_bin : "/work/project/gafl/tools/containers/fastqc_V0.11.8.sif"
multiqc_bin : "/work/project/gafl/tools/containers/multiqc_v1.7.sif"
cutadapt_bin : "/work/project/gafl/tools/containers/cutadapt_v2.7.sif"
fastp_bin : "/work/project/gafl/tools/containers/fastp_0.20.0.sif"
samtools_bin : "/work/project/gafl/tools/containers/samtools_v1.9.sif"
bwa_bin : "/work/project/gafl/tools/containers/bwa_0.7.17.sif"
sambamba_bin : "/work/project/gafl/tools/containers/sambamba_v0.7.1.sif"
gatk4_bin : "/work/project/gafl/tools/containers/gatk4_v4.1.4.1.sif"
R_bin : "/work/project/gafl/tools/containers/R_base_V3.6.0.sif"
# singularity bind for IFB core the home is in: /shared/mfs/data/home
# BIND : "-B /shared/mfs/data/home/jlagnel"
......@@ -69,7 +69,7 @@ R_bin : "/work2/project/gafl/tools/containers/R_base_V3.6.0.sif"
# Bind gafl01:
#BIND : "-B /work/project/gafl,/nosave/project/gafl,/work2/project/gafl"
# bind Genotoul:
BIND : "-B /work2/project/redd_vat_phyton,/work2/project/gafl"
BIND : "-B /work/project/gafl"
# singularity modules only for genotoul
#MODULES : "module load system/singularity-2.5.1"
......
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