updated fastp params

phac-nml · Dec 6, 2023 · 09b6871 · 09b6871
1 parent d3226d5
commit 09b6871
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -200,7 +200,7 @@ params {
         dedup_reads = false
         // -c is used to apply overlap analysis and cut out out adapters
         args {
-            illumina = "--overrepresentation_analysis --trim_poly_g --poly_g_min_len ${params.fastp.polyg_min_len} --trim_poly_x --polyx_min_len ${params.fastp.polyx_min_len} --cut_tail --cut_tail_mean_quality ${params.fastp.cut_tail_mean_quality} --low_complexity_filter --complexity_threshold ${params.fastp.complexity_threshold} --average_qual ${params.fastp.average_quality_e} --cut_mean_quality ${params.fastp.cut_mean_quality} --qualified_quality_phred ${params.fastp.qualified_quality_phred} --unqualified_percent_limit ${params.fastp.unqualified_percent_limit} --length_limit ${params.fastp.illumina_length_max} --length_required ${params.fastp.illumina_length_min} --detect_adapter_for_pe"
+            illumina = "--overrepresentation_analysis --trim_poly_g --poly_g_min_len ${params.fastp.polyg_min_len} --trim_poly_x --polyx_min_len ${params.fastp.polyx_min_len} --cut_tail --cut_tail_mean_quality ${params.fastp.cut_tail_mean_quality} --low_complexity_filter --complexity_threshold ${params.fastp.complexity_threshold} --average_qual ${params.fastp.average_quality_e} --qualified_quality_phred ${params.fastp.qualified_quality_phred} --unqualified_percent_limit ${params.fastp.unqualified_percent_limit} --length_limit ${params.fastp.illumina_length_max} --length_required ${params.fastp.illumina_length_min} --detect_adapter_for_pe"
             single_end = "--overrepresentation_analysis -Q --length_required ${params.fastp.single_end_length_min}"
         }
         report_exclude_fields = ["content_curves", "quality_curves", "GC", "mean", "G", "C", "A", "T", "N", "GC", "kmer_count", "histogram", "overrepresented_sequences"]