release v11.4: Zenodo input link updated

README.md

@@ -56,7 +56,7 @@
 
 <br />
 
-The dataset used in the *nextflow.config* file, as example, is available at https://zenodo.org/records/8403994.
+The dataset used in the *nextflow.config* file, as example, is available at https://zenodo.org/records/14509916/files/ig_clustering_test_1_VH.zip.
 
 <br />
 
@@ -201,7 +201,7 @@ chmod 755 bin/*.*
 ## OUTPUT
 
 
-An example of results obtained with the dataset is present at this address: https://zenodo.org/record/8403994/files/repertoire_profiler.zip
+An example of results obtained with the dataset is present at this address: https://zenodo.org/records/14509864/files/repertoire_profiler_1734454432
 <br /><br />
 Complete informations are in the Protocol 144-rev0 Ig clustering - Immcantation.docx (contact Gael Millot).
 <br /><br />
@@ -298,6 +298,11 @@ Special acknowledgement to [Kenneth Hoehn](https://medicine.yale.edu/profile/ken
 <br /><br />
 ## WHAT'S NEW IN
 
+#### v11.4
+
+- Zenodo input link updated
+
+
 #### v11.3
 
 - Now a zip folder is accepted as input

nextflow.config

@@ -28,7 +28,7 @@
 */
 
 env {
-    sample_path = "https://zenodo.org/records/14500292/files/ig_clustering_test_1_VH.zip" // single character string of the path of the fasta files directory. The last / can be added or not, as it is removed by nextflow file(). Can also be a .zip file that contains only fasta files. Warning: the fasta names must not start by a digit, before alakazam::readChangeoDb() function is fixed by the maintainer. Example : sample_path="/mnt/c/Users/gmillot/Documents/Git_projects/repertoire_profiler/dataset/A1_IgG_H_fw" or sample_path="/pasteur/appa/homes/gmillot/dataset/20210707_AV07016_HAD-III-89_plate3_IgK_sanger_seq". Example with spaces in the path: sample_path="/mnt/x/ROCURONIUM PROJECT/01 Primary data/04.Repertoire analysis/SORT1/SORT1 Seq-original/xlsx_to_fasta_1669018924/All/VL". Example: sample_path = "/mnt/c/Users/gmillot/Documents/Git_projects/repertoire_profiler/dataset/ig_clustering_test_1_VH". Example: sample_path = "https://zenodo.org/records/14500292/files/ig_clustering_test_1_VH.zip"
+    sample_path = "https://zenodo.org/records/14509916/files/ig_clustering_test_1_VH.zip" // single character string of the path of the fasta files directory. The last / can be added or not, as it is removed by nextflow file(). Can also be a .zip file that contains only fasta files. Warning: the fasta names must not start by a digit, before alakazam::readChangeoDb() function is fixed by the maintainer. Example : sample_path="/mnt/c/Users/gmillot/Documents/Git_projects/repertoire_profiler/dataset/A1_IgG_H_fw" or sample_path="/pasteur/appa/homes/gmillot/dataset/20210707_AV07016_HAD-III-89_plate3_IgK_sanger_seq". Example with spaces in the path: sample_path="/mnt/x/ROCURONIUM PROJECT/01 Primary data/04.Repertoire analysis/SORT1/SORT1 Seq-original/xlsx_to_fasta_1669018924/All/VL". Example: sample_path = "/mnt/c/Users/gmillot/Documents/Git_projects/repertoire_profiler/dataset/ig_clustering_test_1_VH". Example: sample_path = "https://zenodo.org/records/14500292/files/ig_clustering_test_1_VH.zip"
     igblast_organism = "mouse" // single character string indicating the organism analyzed. Either "mouse", "human", "rabbit", "rat" or "rhesus_monkey" (value of the --organism option of AssignGenes.py igblast). Example: igblast_organism="human". Example: igblast_organism="mouse"
     igblast_database_path = "germlines/imgt/mouse/vdj" // single character string of the path of the database provided by igblast indicating a folder of fasta files, WITHOUT the last /. Normally, only the organism name should be changed in the path, to be the same as in the igblast_organism parameter. Example: igblast_database_path="germlines/imgt/human/vdj". Example: igblast_database_path="germlines/imgt/mouse/vdj". Warnings (for developers only): (1) see \\wsl$\Ubuntu-20.04\home\gmillot\share for the different possibilities of paths and (2) change this code in the .nf file " MakeDb.py igblast -i \${FILE}_igblast.fmt7 -s ${fs} -r \${REPO_PATH}/imgt_human_IGHV.fasta \${REPO_PATH}/imgt_human_IGHD.fasta \${REPO_PATH}/imgt_human_IGHJ.fasta --extended" if the present path is modified
     igblast_loci = "ig" // single character string of the value of the --loci option of AssignGenes.py igblast. Example: igblast_loci="ig"