From e03a798ff4c4168d14141fa4d81a523bb5b9652c Mon Sep 17 00:00:00 2001
From: hassanfa <hassan.foroughi@gmail.com>
Date: Tue, 22 Dec 2020 13:39:48 +0100
Subject: [PATCH] readlink command fix according to container

---
 BALSAMIC/snakemake_rules/annotation/vep.rule            | 4 ++--
 BALSAMIC/snakemake_rules/quality_control/GATK.rule      | 2 +-
 BALSAMIC/snakemake_rules/variant_calling/split_bed.rule | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/BALSAMIC/snakemake_rules/annotation/vep.rule b/BALSAMIC/snakemake_rules/annotation/vep.rule
index 79f21f516..32b650a7a 100644
--- a/BALSAMIC/snakemake_rules/annotation/vep.rule
+++ b/BALSAMIC/snakemake_rules/annotation/vep.rule
@@ -25,7 +25,7 @@ rule vep_somatic:
   shell:
     """
 source activate {params.conda};
-vep_path=$(dirname $(readlink -e $(which vep)));
+vep_path=$(dirname $(readlink -f $(which vep)));
 tmpvcf={params.tmpvcf};
 export PERL5LIB=;
 vcfanno --base-path {params.ref_path} {params.vcfanno_toml} {input.vcf} \
@@ -101,7 +101,7 @@ rule vep_germline:
   shell:
       """
 source activate {params.conda};
-vep_path=$(dirname $(readlink -e $(which vep)));
+vep_path=$(dirname $(readlink -f $(which vep)));
 export PERL5LIB=;
 vep \
 --dir $vep_path \
diff --git a/BALSAMIC/snakemake_rules/quality_control/GATK.rule b/BALSAMIC/snakemake_rules/quality_control/GATK.rule
index 906e9e6b7..eae6f8343 100644
--- a/BALSAMIC/snakemake_rules/quality_control/GATK.rule
+++ b/BALSAMIC/snakemake_rules/quality_control/GATK.rule
@@ -76,7 +76,7 @@ rule PreparePopVCF:
     benchmark_dir + "PreparePopVCF_" + "tumor_prepare_pop_vcf.tsv"
   shell:
     "source activate {params.conda}; "
-    "readlink -e {input.bam}; "
+    "readlink -f {input.bam}; "
     "bcftools annotate "
         "-x {params.anno_str1}{params.popcode}_AF "
         "{input.ref1kg} "
diff --git a/BALSAMIC/snakemake_rules/variant_calling/split_bed.rule b/BALSAMIC/snakemake_rules/variant_calling/split_bed.rule
index 0f8fbeb97..daa829814 100644
--- a/BALSAMIC/snakemake_rules/variant_calling/split_bed.rule
+++ b/BALSAMIC/snakemake_rules/variant_calling/split_bed.rule
@@ -32,4 +32,4 @@ rule split_bed_by_chrom:
             " > {params.split_bed_dir}$c.{params.origin_bed}; "
         "done; "
         "unset chromlist; "
-        "readlink -e {input.bam}; "
+        "readlink -f {input.bam}; "