From 7efae629bd3349e2586d3553f62566fb862b9a00 Mon Sep 17 00:00:00 2001 From: marcel-keller <61977721+marcel-keller@users.noreply.github.com> Date: Tue, 22 Mar 2022 14:16:43 +0100 Subject: [PATCH] Corrected the --bamutils_clip flags Corrected the --bamutils_clip flags in the tutorials according to parameters tab. I did not check other flags, neither did a test run of the tutorials. --- docs/usage.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index ad427be05..454b10a93 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1272,8 +1272,8 @@ nextflow run nf-core/eager \ --bam_mapping_quality_threshold 25 \ --bam_unmapped_type 'discard' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ <...> ``` @@ -1342,8 +1342,8 @@ nextflow run nf-core/eager \ --bam_mapping_quality_threshold 25 \ --bam_unmapped_type 'discard' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ --run_sexdeterrmine \ --sexdeterrmine_bedfile '../Reference/genome/1240k.sites.bed' \ --run_nuclear_contamination \ @@ -1383,8 +1383,8 @@ nextflow run nf-core/eager \ --bam_mapping_quality_threshold 25 \ --bam_unmapped_type 'discard' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ --run_sexdeterrmine \ --sexdeterrmine_bedfile '../Reference/genome/1240k.sites.bed' \ --run_nuclear_contamination \ @@ -1425,8 +1425,8 @@ nextflow run nf-core/eager \ --bam_mapping_quality_threshold 25 \ --bam_unmapped_type 'discard' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ --run_sexdeterrmine \ --sexdeterrmine_bedfile '../Reference/genome/1240k.sites.bed' \ --run_nuclear_contamination \ @@ -2397,10 +2397,10 @@ nextflow run nf-core/eager \ --run_bedtools_coverage \ --anno_file '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.gff' --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ ---bamutils_clip_none_udg_left 3 \ ---bamutils_clip_none_udg_right 3 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ +--bamutils_clip_double_stranded_none_udg_left 3 \ +--bamutils_clip_double_stranded_none_udg_right 3 \ <...> ``` @@ -2436,10 +2436,10 @@ nextflow run nf-core/eager \ --bam_unmapped_type 'discard' \ --dedupper 'markduplicates' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ ---bamutils_clip_none_udg_left 3 \ ---bamutils_clip_none_udg_right 3 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ +--bamutils_clip_double_stranded_none_udg_left 3 \ +--bamutils_clip_double_stranded_none_udg_right 3 \ --run_bedtools_coverage \ --anno_file '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.gff' \ --run_genotyping \ @@ -2479,10 +2479,10 @@ nextflow run nf-core/eager \ --bam_unmapped_type 'discard' \ --dedupper 'markduplicates' \ --run_trim_bam \ ---bamutils_clip_half_udg_left 2 \ ---bamutils_clip_half_udg_right 2 \ ---bamutils_clip_none_udg_left 3 \ ---bamutils_clip_none_udg_right 3 \ +--bamutils_clip_double_stranded_half_udg_left 2 \ +--bamutils_clip_double_stranded_half_udg_right 2 \ +--bamutils_clip_double_stranded_none_udg_left 3 \ +--bamutils_clip_double_stranded_none_udg_right 3 \ --run_bedtools_coverage \ --anno_file '../Reference/genome/Yersinia_pestis_C092_GCF_000009065.1_ASM906v1.gff' \ --run_genotyping \