minor changes in doc and samples_info files to automatic test

README.md

@@ -124,32 +124,32 @@ DATA:
 
 #### sample_info key
 
-Into the `sample_info` DATA key, you need to give a comma separated `sample_info.txt` file containing information about samples. This file needs header with Forward,Reverse,SampleName,Direction,Treatment,Experiment columns.
+Into the `sample_info` DATA key, you need to give a comma separated `sample_info.txt` file containing information about samples. This file needs header with `SampleName,Forward,Reverse,Treatment,Experiment`  columns.
 
 If you are in single mode, don't fill on 'reverse' column in `sample_info.txt` file 
 
 Here an example for experiment in `single` mode :
 
 ```commandline
-Forward,Reverse,SampleName,Direction,Treatment,Experiment
-/path/to/FASTQ/Batch-rep1_R1.fastq.gz,,Batch_1,R1,Batch,E1
-/path/to/FASTQ/Batch-rep2_R1.fastq.gz,,Batch_2,R1,Batch,E2
-/path/to/FASTQ/Batch-rep3_R1.fastq.gz,,Batch_3,R1,Batch,E3
-/path/to/FASTQ/CENPK-rep1_R1.fastq.gz,,CENPK_1,R1,CENPK,E1
-/path/to/FASTQ/CENPK-rep2_R1.fastq.gz,,CENPK_2,R1,CENPK,E2
-/path/to/FASTQ/CENPK-rep3_R1.fastq.gz,,CENPK_3,R1,CENPK,E3
+SampleName,Forward,Reverse,Treatment,Experiment
+Batch-1,/path/to/FASTQ/Batch-rep1_R1.fastq.gz,,Batch,E1
+Batch-2,/path/to/FASTQ/Batch-rep2_R1.fastq.gz,,Batch,E2
+Batch-3,/path/to/FASTQ/Batch-rep3_R1.fastq.gz,,Batch,E3
+CENPK-1,/path/to/FASTQ/CENPK-rep1_R1.fastq.gz,,CENPK,E1
+CENPK-2,/path/to/FASTQ/CENPK-rep2_R1.fastq.gz,,CENPK,E2
+CENPK-3,/path/to/FASTQ/CENPK-rep3_R1.fastq.gz,,CENPK,E3
 ```
 
 Or `paired` mode ...
 
 ```commandline
-Forward,Reverse,Direction,Treatment,Experiment
-/path/to/FASTQ/Batch-rep1_R1.fastq.gz,/path/to/FASTQ/Batch-rep1_R2.fastq.gz,Batch_1,R1,Batch,E1
-/path/to/FASTQ/Batch-rep2_R1.fastq.gz,/path/to/FASTQ/Batch-rep2_R2.fastq.gz,Batch_2,R1,Batch,E2
-/path/to/FASTQ/Batch-rep3_R1.fastq.gz,/path/to/FASTQ/Batch-rep3_R2.fastq.gz,Batch_3,R1,Batch,E3
-/path/to/FASTQ/CENPK-rep1_R1.fastq.gz,/path/to/FASTQ/CENPK-rep1_R2.fastq.gz,CENPK_1,R1,CENPK,E1
-/path/to/FASTQ/CENPK-rep2_R1.fastq.gz,/path/to/FASTQ/CENPK-rep2_R2.fastq.gz,CENPK_2,R1,CENPK,E2
-/path/to/FASTQ/CENPK-rep3_R1.fastq.gz,/path/to/FASTQ/CENPK-rep3_R2.fastq.gz,CENPK_3,R1,CENPK,E3
+SampleName,Forward,Reverse,Treatment,Experiment
+Batch-1,/path/to/FASTQ/Batch-rep1_R1.fastq.gz,/path/to/FASTQ/Batch-rep1_R2.fastq.gz,Batch,E1
+Batch-2,/path/to/FASTQ/Batch-rep2_R1.fastq.gz,/path/to/FASTQ/Batch-rep2_R2.fastq.gz,Batch,E2
+Batch-3,/path/to/FASTQ/Batch-rep3_R1.fastq.gz,/path/to/FASTQ/Batch-rep3_R2.fastq.gz,Batch,E3
+CENPK-1,/path/to/FASTQ/CENPK-rep1_R1.fastq.gz,/path/to/FASTQ/CENPK-rep1_R2.fastq.gz,CENPK,E1
+CENPK-2,/path/to/FASTQ/CENPK-rep2_R1.fastq.gz,/path/to/FASTQ/CENPK-rep2_R2.fastq.gz,CENPK,E2
+CENPK-3,/path/to/FASTQ/CENPK-rep3_R1.fastq.gz,/path/to/FASTQ/CENPK-rep3_R2.fastq.gz,CENPK,E3
 ```
 
 Finally, you need confirm if reads are paired or single filling in `PAIRED` param using `true` or `false` boolean. If PAIRED : true, samples suffix should be `_R1.fastq.gz` and `_R2.fastq.gz`.

RNAja/install_files/config_test/RNAja-config_paired.yaml

@@ -3,7 +3,7 @@ DATA:
     fastq_dir: "DATA_DIR/DATA_TEST/FASTQ_PAIRED"
     reference: "DATA_DIR/DATA_TEST/REF/GCF_000146045.2_R64_genomic.fna"
     annotation: "DATA_DIR/DATA_TEST/REF/GCF_000146045.2_R64_genomic.gtf"
-    sample_info: "DATA_DIR/DATA_TEST/sample_info.txt"
+    sample_info: "DATA_DIR/DATA_TEST/sample_info_paired.txt"
     de_comparisons: "DATA_DIR/DATA_TEST/treatmentsComparisons.csv"
     output_dir: "RNAJA_OUTPUT"
     PAIRED : true # if true should be _R1 / _R2
@@ -13,7 +13,7 @@ MODE:
     HISAT2_HTSEQCOUNT: false
     STARmap_STARcount: false
     STARmap_HTSEQCOUNT: false
-    STARmap_STRINGTIE: true
+    STARmap_STRINGTIE: false
 
 PARAMS:
     HISAT2:

RNAja/install_files/config_test/RNAja-config_single.yaml

@@ -3,16 +3,16 @@ DATA:
     fastq_dir: "DATA_DIR/DATA_TEST/FASTQ_SINGLE"
     reference: "DATA_DIR/DATA_TEST/REF/GCF_000146045.2_R64_genomic.fna"
     annotation: "DATA_DIR/DATA_TEST/REF/GCF_000146045.2_R64_genomic.gtf"
-    sample_info: "DATA_DIR/DATA_TEST/sample_info.txt"
+    sample_info: "DATA_DIR/DATA_TEST/sample_info_single.txt"
     de_comparisons: "DATA_DIR/DATA_TEST/treatmentsComparisons.csv"
     output_dir: "RNAJA_OUTPUT"
     PAIRED : false # if true should be _R1 / _R2
 
 MODE:
     HISAT2_STRINGTIE: true
-    HISAT2_HTSEQCOUNT: false
-    STARmap_STARcount: false
-    STARmap_HTSEQCOUNT: false
+    HISAT2_HTSEQCOUNT: true
+    STARmap_STARcount: true
+    STARmap_HTSEQCOUNT: true
     STARmap_STRINGTIE: true
 
 PARAMS:
@@ -25,6 +25,6 @@ PARAMS:
         mapping:
             params: "--readFilesCommand zcat" # --outFilterMismatchNoverLmax 0.03
     STRINGTIE:
-        discovery_mode : true
+        discovery_mode : false
     HTSEQCOUNT:
         params: "-s reverse -m union -t gene "