release v3.0: DSL1 -> DSL2 | Two-sided test Fisher test added but remain to be...

release v3.0: DSL1 -> DSL2 | Two-sided test Fisher test added but remain to be control the resulting p value

README.md

@@ -3,7 +3,7 @@
 
 | usage | dependencies |
 | --- | --- |
-| [![Nextflow](https://img.shields.io/badge/code-Nextflow-blue?style=plastic)](https://www.nextflow.io/) | [![Dependencies: Nextflow Version](https://img.shields.io/badge/Nextflow-v21.04.2-blue?style=plastic)](https://github.com/nextflow-io/nextflow) |
+| [![Nextflow](https://img.shields.io/badge/code-Nextflow-blue?style=plastic)](https://www.nextflow.io/) | [![Dependencies: Nextflow Version](https://img.shields.io/badge/Nextflow-v23.04.4-blue?style=plastic)](https://github.com/nextflow-io/nextflow) |
 | [![License: GPL-3.0](https://img.shields.io/badge/licence-GPL%20(%3E%3D3)-green?style=plastic)](https://www.gnu.org/licenses) | |
 
 <br /><br />
@@ -28,6 +28,7 @@
 
 
 - Compute the two-sided Fisher exact test statistics (score) and p values from a vcf annotated file made of patient and control cases.
+- Odds ratio used is (n11/n12)/(n21/n22) = (n11\*n22)/(n12\*n21) with:<br /><ul><li>n11 = nHET_aff + nHOM_ALT_aff (carrier in aff)<br /></li><li>n12 = nHOM_REF_aff (non-carrier in aff)<br /></li><li>n21 = nHET_unaff + nHOM_ALT_unaff (carrier in unaff)<br /></li><li>n22 = nHOM_REF_unaff (non-carrier in unaff)<br /></li>OR > 1 meaning OR in favor of HET+HOM_ALT/aff versus HET+HOM_ALT/unaff
 - Return a res.tsv file and a Miami plot.
 - The tsv file can include fields and sub-fields of the vcf file in different columns. See the tsv_extra_fields parameter of the nextflow.config file, as well as the OUTPUT section below.
 - Return also a res.vcf file made from the res.tsv file, mimicing a VCF file, i.e., with the inital header of the .vcf and with the fisher results added in the INFO section.
@@ -295,6 +296,12 @@ The developers & maintainers of the mentioned softwares and packages, including:
 <br /><br />
 ## WHAT'S NEW IN
 
+### v3.0
+
+- DSL1 -> DSL2.
+- Two-sided test Fisher test added but remain to be control the resulting p value.
+
+
 ### v2.5
 
 - .config improved

bin/fisher_lod.py

@@ -160,7 +160,7 @@ csq_subfield_pos = [26]
                     an+=1
         # une fois que l'on a lu les information pour tous les individus, nous calculons le Fisher
         # ici c'est porteur (gt 1 ou 3) versus non porteur (gt 0) pour les atteints (aff) versus les non atteint (una)
-        oddsratio, pvalue = stats.fisher_exact([[aff.get(1,0)+aff.get(3,0),aff.get(0,0)],[una.get(1,0)+una.get(3,0),una.get(0,0)]])
+        oddsratio, pvalue = stats.fisher_exact([[aff.get(1,0)+aff.get(3,0),aff.get(0,0)],[una.get(1,0)+una.get(3,0),una.get(0,0)]], alternative='two-sided')
 
         # filling a one row data frame with or without adding
         tempo_csq = v.INFO.get('CSQ').split(',') # number of fields in CSQ (comma sep), i.e., nb of rows

nextflow.config

@@ -172,19 +172,19 @@ process {
     withLabel: bash {
         container='gmillot/htslib_v1.0:gitlab_v9.1'
         cpus=1 // only used when name = "local" in the executor part above
-        memory='64G' // only used when name = "local" in the executor part above
+        memory='60G' // only used when name = "local" in the executor part above
     }
 
     withLabel: python {
         container='gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7'
         cpus=1 // only used when name = "local" in the executor part above
-        memory='64G' // only used when name = "local" in the executor part above
+        memory='60G' // only used when name = "local" in the executor part above
     }
 
     withLabel: r_ext {
         container='gmillot/r_v4.1.2_extended_v2.1:gitlab_v8.8'
         cpus=1 // only used when name = "local" in the executor part above
-        memory='64G' // only used when name = "local" in the executor part above
+        memory='60G' // only used when name = "local" in the executor part above
     }
 }