helix update

README.md

@@ -139,7 +139,7 @@ nextflow run -hub pasteur gmillot/micmac -r v1.0.0
 Copy-paste this after having modified the EXEC_PATH variable:
 
 <pre>
-EXEC_PATH="/pasteur/zeus/projets/p01/BioIT/gmillot/micmac" # where the bin folder of the main.nf script is located
+EXEC_PATH="/pasteur/helix/projects/BioIT/gmillot/micmac" # where the bin folder of the main.nf script is located
 export CONF_BEFORE=/opt/gensoft/exe # on maestro
 
 export JAVA_CONF=java/13.0.2
@@ -164,7 +164,7 @@ Modify the second line of the code below, and run from where the *main.nf* and *
 
 <pre>
 HOME_INI=$HOME
-HOME="${ZEUSHOME}/micmac/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/micmac/, for instance. See NFX_HOME in the nextflow software script
+HOME="${HELIXHOME}/micmac/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/micmac/, for instance. See NFX_HOME in the nextflow software script
 trap '' SIGINT
 nextflow run --modules ${MODULES} main.nf -c nextflow.config
 HOME=$HOME_INI
@@ -179,7 +179,7 @@ Modify the first and third lines of the code below, and run (results will be whe
 <pre>
 VERSION="v1.0"
 HOME_INI=$HOME
-HOME="${ZEUSHOME}/micmac/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/micmac/, for instance. See NFX_HOME in the nextflow software script
+HOME="${HELIXHOME}/micmac/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/micmac/, for instance. See NFX_HOME in the nextflow software script
 trap '' SIGINT
 nextflow run --modules ${MODULES} -hub pasteur gmillot/micmac -r $VERSION -c $HOME/nextflow.config
 HOME=$HOME_INI
@@ -242,7 +242,7 @@ The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/micma
 
 This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose.
-See the GNU General Public License for more details at https://www.gnu.org/licenses.
+See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.
 
 <br /><br />
 ## CITATION

nextflow.config

@@ -28,7 +28,7 @@
 */
 
 env {
-    sample_path = "/mnt/c/Users/gmillot/Documents/Git_projects/micmac/dataset/test" // single character string of the path of the files directory. The last / can be added or not, as it is removed by nextflow file(). Example (leave the spaces in the path as they are): sample_path="/mnt/c/Users/gmillot/Documents/Git_projects/micmac/dataset/20240718_dataset". Example: sample_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/micmac/dataset/pour_gael"
+    sample_path = "/mnt/c/Users/gmillot/Documents/Git_projects/micmac/dataset/test" // single character string of the path of the files directory. The last / can be added or not, as it is removed by nextflow file(). Example (leave the spaces in the path as they are): sample_path="/mnt/c/Users/gmillot/Documents/Git_projects/micmac/dataset/20240718_dataset". Example: sample_path = "/pasteur/helix/projects/BioIT/gmillot/micmac/dataset/pour_gael"
     mat_sep = " " // single character string of the separator in the file. Example: mat_sep = " "
     mat_header = "X_CONTIG X_CONTIG_SIZE X_MAG Y_CONTIG Y_CONTIG_SIZE Y_MAG COUNT" // single character string of the names to add to the columns of the file. Example: mat_header = "X_CONTIG X_CONTIG_SIZE X_MAG Y_CONTIG Y_CONTIG_SIZE Y_MAG COUNT". Warning: use a single space between string.
 }
@@ -72,8 +72,8 @@ env{
     cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v12.8/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }
 
-apptainer_path = "NULL" // single character string of the path of the apptainer folder (where all the apptainer images are are pulled and stored for proper nextflow execution). Write "NULL" for default path (but will not work in most cases). Example: apptainer_path='/pasteur/zeus/projets/p01/BioIT/gmillot/apptainer'. Example: apptainer_path='/mnt/c/Users/gmillot/apptainer'. Example: apptainer_path="$projectDir/apptainer" # do not forget double quotes
-out_path_ini = "$projectDir/results" // single character string of where the output files will be saved. Example out_path_ini = '.' for where the main.nf run is executed or out_path_ini = "$projectDir/results" to put the results in a result folder (created if required), $projectDir indicating where the main.nf run is executed. Example: out_path_ini = '/mnt/c/Users/Gael/Desktop'. Example : out_path_ini="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results". Warning: this does not work: out_path_ini = "/mnt/share/Users/gael/Desktop"
+apptainer_path = "NULL" // single character string of the path of the apptainer folder (where all the apptainer images are are pulled and stored for proper nextflow execution). Write "NULL" for default path (but will not work in most cases). Example: apptainer_path='/pasteur/helix/projects/BioIT/gmillot/apptainer'. Example: apptainer_path='/mnt/c/Users/gmillot/apptainer'. Example: apptainer_path="$projectDir/apptainer" # do not forget double quotes
+out_path_ini = "$projectDir/results" // single character string of where the output files will be saved. Example out_path_ini = '.' for where the main.nf run is executed or out_path_ini = "$projectDir/results" to put the results in a result folder (created if required), $projectDir indicating where the main.nf run is executed. Example: out_path_ini = '/mnt/c/Users/Gael/Desktop'. Example : out_path_ini="/pasteur/helix/projects/BioIT/gmillot/08002_bourgeron/results". Warning: this does not work: out_path_ini = "/mnt/share/Users/gael/Desktop"
 result_folder_name="micmac" // single character string.of the name of the folder where the results files are dorpped
 
 
@@ -165,7 +165,7 @@ apptainer {
     //runOptions = '--home $HOME:/home/$USER --bind /pasteur' // provide any extra command line options supported by the apptainer exec. Here, fait un bind de tout /pasteur dans /pasteur du container. Sinon pas d accès
     if(apptainer_path == "NULL"){
         if(system_exec == 'slurm'){
-            cacheDir = '/pasteur/zeus/projets/p01/BioIT/gmillot/apptainer' // name of the directory where remote Singularity images are stored. When rerun, the exec directly uses these without redownloading them. When using a computing cluster it must be a shared folder accessible to all computing nodes
+            cacheDir = '/pasteur/helix/projects/BioIT/gmillot/apptainer' // name of the directory where remote Singularity images are stored. When rerun, the exec directly uses these without redownloading them. When using a computing cluster it must be a shared folder accessible to all computing nodes
         }else if(system_exec == 'slurm_local'){
             cacheDir = 'apptainer' // "$projectDir/apptainer" can be used but do not forget double quotes.
         }else{