diff --git a/README.md b/README.md
index 49662450ade574007faa07b482ea9c35326dc40a..1195b73dc1e2b069becd524ff08e3e63edf8731e 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # Synteny pipeline
-This Nextflow pipeline can produce orthogroups from OrthoFinder and synteny blocks from MCScanX, using genome and associated annotation file.
+This Nextflow pipeline can produce orthogroups from OrthoFinder and synteny blocks from MCScanX, using genome and associated annotation file!
 
 ![metro](fig/metro_v2.png)
 
@@ -28,12 +28,6 @@ sp2   input/sp2.fa     input/sp2.gff3   input/chr_conversion/sp2.tsv
 The ID of each species should be unique and will be used to name output files.
 Please see the `example_data/synteny_protein_infiles.tsv` for a working template.
 
-
-## Softwares
-All tools required for the pipeline execution will be installed on launch with Conda (ensure you have it installed) or Docker, with the exception of MCScanX.
-MCScanX should be installed in the bin/ folder of the pipeline, from https://github.com/wyp1125/MCScanX/archive/refs/heads/master.zip, unzipped, then `make` (ensure javac is installed). In case of difficulty, refer to the steps described here (https://github.com/wyp1125/MCScanX#installation).
-The programm should be accessed through bin/MCScanX-master/McScanX.
-
 # Running the pipeline
 An example dataset is provided to test the pipeline.
 With the first mode:
diff --git a/main.nf b/main.nf
index c585213ed21de378f8688fc9ea3184c232cfe7cb..6581bce23f6746d031651bf8dcac562c859f42ea 100644
--- a/main.nf
+++ b/main.nf
@@ -66,7 +66,6 @@ workflow {
         //     }
         // collect all proteome to a channel to give to OrthoFinder
         prot_ch = prepare_species_genome_files.out.protein
-        prot_ch.view()
         gff3_ch = prepare_species_genome_files.out.gff3
 
     } else if (params.species_protein_files) {
@@ -82,7 +81,6 @@ workflow {
         .collect()
         .set { ready_prot_ch }
 
-    ready_prot_ch.view()
     //*******************//
     // Orthogroups comp. //
     //*******************//
diff --git a/modules/runMCScanX.nf b/modules/runMCScanX.nf
index 5520803f03f4de403d451aa16b2a5e0a2a98c099..c7aff257ab4a9d711c8914b0fbb1948ab984b4bb 100644
--- a/modules/runMCScanX.nf
+++ b/modules/runMCScanX.nf
@@ -5,7 +5,7 @@
 process runMCScanX {
     //label 'medium'
     // container 'ghcr.io/wyp1125/mcscanx/run-on-arch-wyp1125-mcscanx-ci-aarch64-ubuntu20-04:latest'
-    conda ''
+    conda 'bioconda::mcscanx=1.0.0'
 
     input:
     path blast
@@ -21,7 +21,7 @@ process runMCScanX {
     mv $blast \${prefix}.blast
     mv $gff \${prefix}.gff
 
-    ${params.project_dir}/bin/MCScanX-master/MCScanX \
+    MCScanX \
     ./\$prefix \
     -k ${params.s_match_score} \
     -g ${params.s_gap_penalty} \
diff --git a/modules/runOrthoFinder.nf b/modules/runOrthoFinder.nf
index 2516cb6810341917dc52d5bac9adbff6d76f823c..5bfb5d35aa1487abbacadb77fc6ba49058c9e6a7 100644
--- a/modules/runOrthoFinder.nf
+++ b/modules/runOrthoFinder.nf
@@ -4,8 +4,8 @@
 
 process runOrthoFinder {
     //label 'medium'
-    //container 'quay.io/biocontainers/orthofinder:2.5.5--hdfd78af_1'
-    conda 'bioconda::orthofinder=2.5.5'
+    container 'quay.io/biocontainers/orthofinder:2.5.5--hdfd78af_1'
+    //conda 'bioconda::orthofinder=2.5.5'
 
     input:
     path "*"