fix: FusionInspector comes with STAR-Fusion by default

nf-core · May 6, 2020 · 49e695b · 49e695b
1 parent b579d71
commit 49e695b
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Showing 3 changed files with 8 additions and 15 deletions.
diff --git a/containers/star-fusion/Dockerfile b/containers/star-fusion/Dockerfile
@@ -10,17 +10,11 @@ RUN conda env create -f /environment.yml && conda clean -a
 # Add conda installation dir to PATH (instead of doing 'conda activate')
 ENV PATH /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/bin:$PATH
 
-# ctat-genome-lib-builder
-RUN cd /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/ && \
-    wget https://github.com/NCIP/ctat-genome-lib-builder/archive/2830cd708c5bb9353878ca98069427e83acdd625.zip && \
-    unzip 2830cd708c5bb9353878ca98069427e83acdd625.zip && \
-    cd ctat-genome-lib-builder-2830cd708c5bb9353878ca98069427e83acdd625 && \
-    rm /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/bin/prep_genome_lib.pl
-
-ENV PATH /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/ctat-genome-lib-builder-2830cd708c5bb9353878ca98069427e83acdd625/:$PATH
+# FusionInspector
+ENV PATH /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/STAR-Fusion/FusionInspector:$PATH
 
-RUN ln -s /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/libssl.so /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/libssl.so.1.0.0 && \
-    ln -s /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/libcrypto.so /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/libcrypto.so.1.0.0
+# ctat-genome-lib-builder
+ENV PATH /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/lib/STAR-Fusion/ctat-genome-lib-builder:$PATH
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-rnafusion-star-fusion_1.8.1 > nf-core-rnafusion-star-fusion_1.8.1.yml
diff --git a/containers/star-fusion/environment.yml b/containers/star-fusion/environment.yml
@@ -7,7 +7,5 @@ dependencies:
   - bioconda::dfam=2.0
   - bioconda::hmmer=3.2.1
   - bioconda::star-fusion=1.8.1
-  - bioconda::fusion-inspector=2.2.1
   - bioconda::trinity=2.6.6
-  - conda-forge::perl-carp-assert
-  - conda-forge::unzip=6.0
+  - conda-forge::perl-carp-assert
diff --git a/main.nf b/main.nf
@@ -709,7 +709,7 @@ process fusion_inspector {
         file(reference) from reference.fusion_inspector
 
     output:
-        file("*.{fa,gtf,bed,bam,bai,txt}") into fusion_inspector_output
+        file("*.{fa,gtf,bed,bam,bai,txt,html}") into fusion_inspector_output
 
     when: params.fusion_inspector && (!params.single_end || params.debug)
 
@@ -722,8 +722,9 @@ process fusion_inspector {
         --left_fq ${reads[0]} \\
         --right_fq ${reads[1]} \\
         --CPU ${task.cpus} \\
-        --out_dir . \\
+        -O . \\
         --out_prefix finspector \\
+        --vis \\
         ${extra_params} 
     """
 }