Merge branch 'main' of github.com:Juke34/AliNe

Author: Juke34

README.md

@@ -234,7 +234,7 @@ Please follow the instructions at the [Singularity website](https://docs.sylabs.
 You can first check the available options and parameters by running:
 
 ```bash
-nextflow run Juke34/AliNe -r v1.4.0 --help
+nextflow run Juke34/AliNe -r v1.5.0 --help
 ```
 
 ### Profile
@@ -246,7 +246,7 @@ To run the workflow you must select a profile according to the container platfor
 The command will look like that: 
 
 ```bash
-nextflow run Juke34/AliNe -r v1.4.0 -profile docker <rest of paramaters>
+nextflow run Juke34/AliNe -r v1.5.0 -profile docker <rest of paramaters>
 ```
 
 Another profile is available (/!\\ actually not yet implemented):
@@ -256,7 +256,7 @@ Another profile is available (/!\\ actually not yet implemented):
 The use of the `slurm` profile  will give a command like this one:
 
 ```bash
-nextflow run Juke34/AliNe -r v1.4.0 -profile singularity,slurm <rest of paramaters>
+nextflow run Juke34/AliNe -r v1.5.0 -profile singularity,slurm <rest of paramaters>
 ```
 
 ### Example
@@ -266,7 +266,7 @@ Here, we use the docker container platform, remote read and reference files, spe
 
 ```bash
 nextflow run Juke34/AliNe \
-  -r v1.4.0 \
+  -r v1.5.0 \
   -profile docker \
   --reads https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R1.fastq.gz \
   --reference https://raw.githubusercontent.com/Juke34/AliNe/refs/heads/main/test/yeast.fa \
@@ -285,25 +285,25 @@ Test data are included in the AliNe repository in the `test` folder.
 Test with short single reads:
 
 ```bash
-nextflow run -profile docker,test_illumina_single Juke34/AliNe -r v1.4.0
+nextflow run -profile docker,test_illumina_single Juke34/AliNe -r v1.5.0
 ```
 
 Test with short paired reads:
 
 ```bash
-nextflow run -profile docker,test_illumina_paired Juke34/AliNe -r v1.4.0
+nextflow run -profile docker,test_illumina_paired Juke34/AliNe -r v1.5.0
 ```
 
 Test with ont reads:
 
 ```bash
-nextflow run -profile docker,test_ont Juke34/AliNe -r v1.4.0
+nextflow run -profile docker,test_ont Juke34/AliNe -r v1.5.0
 ```
 
 Test with pacbio reads:
 
 ```bash
-nextflow run -profile docker,test_pacbio Juke34/AliNe -r v1.4.0
+nextflow run -profile docker,test_pacbio Juke34/AliNe -r v1.5.0
 ```
 
 On success you should get a message looking like this:

aline.nf

@@ -1456,26 +1456,21 @@ workflow.onComplete {
 /*
 Other aligner?
  - to map ont?
- - Check salmon can be used as aligner?
  - dragmap 
- - bowtie1
- 
-Annotation:
-Star: When annotation is provided star will need read length information to index the reference. 
-If no read length provided by the user and several fastq files are provided, only the first one will be used to get the read length (we perform only one index).
 
 How to add an aliger ?
+-----------------------
 Add a module,
 In aline.nf 
     Add the aligner in the aligner_list
     Import module here
-    If behaves differently depending sequencing techniology add condition in the PARAMS CHECK section
+    If behaves differently depending sequencing techniology add condition in the PARAMS CHECK sections (module bash.nf)
     If tool need read length guessing add it in the LIBRARY TYPE GUESSING to activate the guessing if read length not provided by user.
     Add in help
     Add in printAlignerOptions
-    Add process in the workflow align
+    Add aligner process in the main workflow 
     Think to convert sam to bam if necessary
     Think to sort bam output if necessary 
 Add info in README.md
 Add tool in multiqc config file (at least for fastqc)
-*/
+*/