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Commit dadbebbc authored by aliarifki's avatar aliarifki
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Suppression de l'option config_file

parent 662bcfc8
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...@@ -264,7 +264,7 @@ workflow { ...@@ -264,7 +264,7 @@ workflow {
//####################### PREPROCESSING ####################### //####################### PREPROCESSING #######################
/*
//Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs) //Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp) seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
...@@ -276,7 +276,7 @@ workflow { ...@@ -276,7 +276,7 @@ workflow {
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect()) hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
sort_index_bam(hbv_genome.out.bam) sort_index_bam(hbv_genome.out.bam)
//il faut ajouter une boucle if pour le mode cpu/gpu //il faut ajouter une boucle if pour le mode cpu/gpu
control_bam(ss.collect(), sort_index_bam.out.indexed_bam) //control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
//###################### START POSITIONS ####################### //###################### START POSITIONS #######################
...@@ -300,5 +300,5 @@ workflow { ...@@ -300,5 +300,5 @@ workflow {
.set{files_for_rna_count} .set{files_for_rna_count}
rna_count(files_for_rna_count) rna_count(files_for_rna_count)
*/
} }
...@@ -141,8 +141,7 @@ guppy_barcoder \ ...@@ -141,8 +141,7 @@ guppy_barcoder \
--input_path ${pass_path} \ --input_path ${pass_path} \
--save_path . \ --save_path . \
-t ${params.gpu_threads_per_caller} \ -t ${params.gpu_threads_per_caller} \
--config ${params.config_file} \ --barcode_kits ${params.kit_barcoding} \
#--barcode_kits ${params.kit_barcoding} \
--progress_stats_frequency 60 \ --progress_stats_frequency 60 \
--enable_trim_barcodes \ --enable_trim_barcodes \
--trim_adapters \ --trim_adapters \
......
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