From afe6f2a6743f807250275aecf7944fae80a70fdc Mon Sep 17 00:00:00 2001
From: FerriolCalvet <ferriolcalvet@gmail.com>
Date: Mon, 16 Jan 2023 23:07:02 +0100
Subject: [PATCH] Fixing bug in docker file and in container selection of
 subworkflow

---
 docker/geneidx/Dockerfile | 5 -----
 nextflow.config           | 1 -
 subworkflows/tools.nf     | 2 +-
 3 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/docker/geneidx/Dockerfile b/docker/geneidx/Dockerfile
index 59b0bbe..756ffa3 100644
--- a/docker/geneidx/Dockerfile
+++ b/docker/geneidx/Dockerfile
@@ -44,8 +44,3 @@ RUN chmod +x /usr/local/bin/FastaToTbl
 
 RUN chmod +x /usr/local/bin/sgp_getHSPSR.pl
 
-
-ENTRYPOINT [ "/usr/local/bin/blast2gff" ]
-ENTRYPOINT [ "/usr/local/bin/FastaToTbl" ]
-ENTRYPOINT [ "/usr/local/bin/geneid" ]
-ENTRYPOINT [ "/usr/local/bin/sgp_getHSPSR.pl" ]
diff --git a/nextflow.config b/nextflow.config
index 7569ad6..dd66f34 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,7 +13,6 @@ includeConfig 'conf/base.config'
 
 process {
     // indicates the default container to be used if not defined within the modules
-    // container = 'ferriolcalvet/geneid-fetching:latest'
     container = 'ferriolcalvet/geneidx:latest'
 
     // custom container options in case you use docker for mapping the users and avoid docker writing files as root
diff --git a/subworkflows/tools.nf b/subworkflows/tools.nf
index 2d3b69f..58536c8 100644
--- a/subworkflows/tools.nf
+++ b/subworkflows/tools.nf
@@ -64,7 +64,7 @@ process fix_chr_names {
 process Index_i {
 
     // indicates to use as a container the value indicated in the parameter
-    container "ferriolcalvet/geneid-fetching"
+    container "ferriolcalvet/geneidx"
 
     // indicates to use as a label the value indicated in the parameter
     label (params.LABEL)