Clean params deprecated.

src/bolero.nf

@@ -110,6 +110,7 @@ params.seqkit_grep_out = "03_fastq/"
 params.porechop_out = "03_fastq/"
 params.cutadapt_out = "04_cutadapt/"
 params.minimap2_genome_out = "05_minimap2/"
+params.indexed_bam_out = "05_minimap2/"
 params.filtered_bam_out = "05_minimap2/"
 params.start_position_counts_out = "06_start_positions/"
 params.nanosplicer_out = "07_nanosplicer/"
@@ -183,9 +184,7 @@ include { concatenate } from "./nf_modules/concatenate/main.nf"
 include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
 include { hbv_genome } from "./nf_modules/minimap2/main.nf"
 include { seqkit_grep } from "./nf_modules/seqkit/main.nf"
-include { sort_bam } from './nf_modules/samtools/main.nf' addParams(sort_bam_out: params.minimap2_genome_out)
-include { index_bam } from './nf_modules/samtools/main.nf' addParams(index_bam_out: params.minimap2_genome_out)
-include { sort_index_bam } from './nf_modules/samtools/main.nf' addParams(indexed_bam_out: params.minimap2_genome_out)
+include { sort_index_bam } from './nf_modules/samtools/main.nf'
 include { filter_as } from './nf_modules/samtools/main.nf'
 include { start_position_counts } from "./nf_modules/samtools/main.nf"
 include { start_position_individuals } from "./nf_modules/start_positions/main.nf"