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readlink command fix according to container #533

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Dec 22, 2020
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4 changes: 2 additions & 2 deletions BALSAMIC/snakemake_rules/annotation/vep.rule
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ rule vep_somatic:
shell:
"""
source activate {params.conda};
vep_path=$(dirname $(readlink -e $(which vep)));
vep_path=$(dirname $(readlink -f $(which vep)));
tmpvcf={params.tmpvcf};
export PERL5LIB=;
vcfanno --base-path {params.ref_path} {params.vcfanno_toml} {input.vcf} \
Expand Down Expand Up @@ -101,7 +101,7 @@ rule vep_germline:
shell:
"""
source activate {params.conda};
vep_path=$(dirname $(readlink -e $(which vep)));
vep_path=$(dirname $(readlink -f $(which vep)));
export PERL5LIB=;
vep \
--dir $vep_path \
Expand Down
2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/quality_control/GATK.rule
Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ rule PreparePopVCF:
benchmark_dir + "PreparePopVCF_" + "tumor_prepare_pop_vcf.tsv"
shell:
"source activate {params.conda}; "
"readlink -e {input.bam}; "
"readlink -f {input.bam}; "
"bcftools annotate "
"-x {params.anno_str1}{params.popcode}_AF "
"{input.ref1kg} "
Expand Down
2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/variant_calling/split_bed.rule
Original file line number Diff line number Diff line change
Expand Up @@ -32,4 +32,4 @@ rule split_bed_by_chrom:
" > {params.split_bed_dir}$c.{params.origin_bed}; "
"done; "
"unset chromlist; "
"readlink -e {input.bam}; "
"readlink -f {input.bam}; "