From 92baa4d08228b23ff96972a0cbc9a54c3c92a59d Mon Sep 17 00:00:00 2001 From: Schultheis Date: Thu, 6 Dec 2018 14:32:46 +0100 Subject: [PATCH] added parameter to list and description --- pipeline.nf | 33 ++++++++++++++++++++++++++------- 1 file changed, 26 insertions(+), 7 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 0ebc301..f12edad 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -23,10 +23,19 @@ params.config="" params.max_size_fp=100 //clustering - params.sequence_coverage=8 - - params.kmer=10 - params.aprox_motif_len=10 + //reduce_bed + params.kmer=10 + params.aprox_motif_len=10 + params.motif_occurence=1 + params.min_seq_length=10 + + //cdhit_wrapper + params.global=0 + params.identity=0.8 + params.sequence_coverage=8 + params.memory=800 + params.throw_away_seq=9 + params.strand=0 //motif_estimation //bed_to_clustered_fasta @@ -67,9 +76,19 @@ Optional arguments: --max_size_fp INT (Default: 100) Clustering: - --sequence_coverage INT (Default: 8) - --kmer INT (Default: 10) - --aprox_motif_len INT (Default: 10) + Sequence preparation/ reduction: + --kmer INT Kmer length (Default: 10) + --aprox_motif_len INT Motif length (Default: 10) + --motif_occurence FLOAT Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif. + --min_seq_length INT Remove all sequences below this value. (Default: 10) + + Clustering: + --global INT Global (=1) or local (=0) alignment. (Default: 0) + --identity FLOAT Identity threshold. (Default: 0.8) + --sequence_coverage INT Minimum aligned nucleotides on both sequences. (Default: 8) + --memory INT Memory limit in MB. 0 for unlimited. (Default: 800) + --throw_away_seq INT Remove all sequences equal or below this length before clustering. (Default: 9) + --strand INT Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0) Motif estimation: --motif_min_len INT Minimum length of Motif (Default: 8)