revert: lofreq!

CCBR · May 30, 2024 · 0033918 · 0033918
1 parent d3f0ae8
commit 0033918
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Showing 3 changed files with 2 additions and 13 deletions.
diff --git a/conf/containers.config b/conf/containers.config
@@ -2,7 +2,7 @@
 params {
     containers {
         base = 'docker://nciccbr/ccbr_ubuntu_base_20.04:v6.1'
-        logan = 'docker://dnousome/ccbr_logan_base:v0.3.4'
+        logan = 'docker://dnousome/ccbr_logan_base:v0.3.5'
         vcf2maf = 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
         lofreq = 'docker://dnousome/ccbr_lofreq:v0.0.1'
         octopus = 'docker://dancooke/octopus:latest'

diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile
@@ -192,16 +192,6 @@ RUN wget -O svaba_1.2.0 https://github.com/walaj/svaba/releases/download/v1.2.0/
 
 ENV PATH="/opt2/svaba:$PATH"
 
-# LOFREQ
-RUN git clone https://github.com/CSB5/lofreq \
-    && cd /opt2/lofreq \
-    && ./bootstrap \
-    && ./configure --prefix=/opt2/lofreq/ \
-    && make \
-    && make install 
-
-ENV PATH="/opt2/lofreq/bin:$PATH"
-
 # MUSE
 RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v2.0.4.tar.gz \
     && tar -xzf muse_2.0.4.tar.gz \ 

diff --git a/modules/local/variant_calling.nf b/modules/local/variant_calling.nf
@@ -520,7 +520,7 @@ script:
 
 
 process lofreq_tn {
-    container "${params.containers.logan}"
+    container "${params.containers.lofreq}"
     label 'process_somaticcaller'
 
     input:
@@ -529,7 +529,6 @@ process lofreq_tn {
 
 
     output:
-
         tuple val(tumorname), val(normalname),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.snvs.vcf.gz"),
         path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.snvs.vcf.gz"),