Make params file usable in command line

README.md

@@ -19,7 +19,27 @@ An example of the params.config and fastqScreen are available in the assets fold
 
 Example of a basic command line the launch the pipeline is (from the nextflow folder) :  
 ```bash 
-sbatch -J nf-illumina_BHNKY7DRX2_1 -p wflowq -t 3-00 --mem 5GB --wrap="module load bioinfo/Nextflow-v21.04.1; cd /home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x/nextflow; nextflow run /work/sbsuser/test/jules/VisualStudioSources/wf-illumina-nf/main.nf -profile prod -ansi-log false"
+sbatch -J nf-illumina_BHNKY7DRX2_1 -p wflowq -t 3-00 --mem 5GB --wrap="module load bioinfo/Nextflow-v21.04.1; cd /home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x/nextflow; nextflow run /work/sbsuser/test/jules/VisualStudioSources/wf-illumina-nf/main.nf -profile prod -ansi-log false -params-file ../params.yml"
 ```
 
+Tha YAML parameter file must looks like :
+```
+inputdir: "/home/sbsuser/work/Nextflow/wf-illumina-nf/data_test/NovaSeq/211129_A00318_0259_AHNMTTDSX2_Lane1_1638345606_dna"
+project: 'GwOAK_small'
+isMultiplex: true
+dataNature: "DNA"
+pairedEnd: true
+splitReads: true #      // ????
+referenceGenome: "/save/ng6/TODO/HiSeqIndexedGenomes/new_struct/Quercus_robur/genome/GCA_900291515.1/BWA/GCA_900291515.1_Q_robur_v1_genomic.fna"
+addBankForConta: ""
+runName: "ContaComparison"
+sequencer: "NovaSeq"
+run_date: "2022"
+machineID: "NOVA"
+fcID: "HNMTTDSX2"
+lane: "1"
+demuxUniqueness: "1638345606"
+```
+
+
 NB : for the moment, the case of multi-projects lane is not managed !
\ No newline at end of file

assets/_email_template.txt

-----------------------------------------------------
-  GeT/template v${version}
-----------------------------------------------------
-
-Run Name: $runName
-
-<% if (success){
-    out << "## GeT/template execution completed successfully! ##"
-} else {
-    out << """####################################################
-## GeT/template execution completed unsuccessfully! ##
-####################################################
-The exit status of the task that caused the workflow execution to fail was: $exitStatus.
-The full error message was:
-
-${errorReport}
-"""
-} %>
-
-
-The workflow was completed at $dateComplete (duration: $duration)
-
-The command used to launch the workflow was as follows:
-
-  $commandLine
-
-
-
-Pipeline Configuration:
------------------------
-<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
-
---
-GeT/template
-https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf

assets/params.yml_example

+
+inputdir="/home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x"
+project = "MAGICs"
+isMultiplex = true
+dataNature = "DNA"
+splitReads = true
+referenceGenome = ""
+addBankForConta = ""
+runName="Test_10X"
+sequencer="NovaSeq"
+run_date="230116"
+machineID="NOVA"
+fcID="BHNKY7DRX2"
+lane="1"
+demuxUniqueness="1673933427"

conf/base.config

@@ -10,13 +10,14 @@ params {
 	outdir = "./"			// base output directory for all analysis
 }
 
-import java.text.SimpleDateFormat
-SimpleDateFormat uniqueness_format = new SimpleDateFormat("yyyMMddHHmmss")
+params.samplesheet = params.inputdir.toString() + "/SampleSheet.csv"
+params.data = params.inputdir.toString() + "/" + params.project.toString()
 
-System.out.println "Lecture du fichier de configuration du run : $launchDir/../params.config"
-includeConfig "$launchDir/../params.config"
+System.out.println "Lecture du fichier de configuration du run : PARAMS"
 
 // Dynamic params
+import java.text.SimpleDateFormat
+SimpleDateFormat uniqueness_format = new SimpleDateFormat("yyyyMMddHHmmss")
 params {
 	nf_uniqueness = uniqueness_format.format(new Date())
 	outdir= params.inputdir + "/nextflow/" + nf_uniqueness