From 76b07f929fe19375166e7288c325a24a4dafa97f Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Sat, 15 Dec 2018 23:09:35 +0100 Subject: [PATCH 1/2] Update pipeline.nf --- pipeline.nf | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index ad4b199..71709f9 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -9,6 +9,7 @@ params.tfbs_path="" params.create_known_tfbs_path = "./" params.help = 0 + params.out = "./out/" //peak_calling params.window_length = 200 @@ -57,9 +58,9 @@ params.organism="hg38" params.tissue="" -if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" == "1"){ +if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0"){ log.info """ -Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] +Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file] Required arguments: --bigwig Path to BigWig-file @@ -69,9 +70,12 @@ Required arguments: --config Path to UROPA configuration file --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. Path can be set as tfbs_path in next run. (Default: './') + --out Output Directory (Default: './out/') + Optional arguments: - - --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. + + --help [0|1] 1 to show this help message. (Default: 0) + --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) From e0ec81bee9d9358d30bda5107eabe65ce75653a5 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Sat, 15 Dec 2018 23:10:12 +0100 Subject: [PATCH 2/2] Update README.md --- README.md | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index a3c4947..1aa01e6 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ When the enviroment is created, set the variable 'path_env' in the configuration ## Quick Start ```console -nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] +nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file] ``` ## Parameters For a detailed overview for all parameters follow this [link](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki/Configuration). @@ -54,26 +54,29 @@ Required arguments: --config Path to UROPA configuration file --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. Path can be set as tfbs_path in next run. (Default: './') + --out Output Directory (Default: './out/') + Optional arguments: - - --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. + --help [0|1] 1 to show this help message. (Default: 0) + --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. + Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) --step INT This parameter sets the number of positions to slide the window forward. (Default: 100) --percentage INT Threshold in percent (Default: 0) - + Filter unknown motifs: --min_size_fp INT Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10) --max_size_fp INT Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100) - + Clustering: 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 Interations 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) @@ -81,7 +84,7 @@ Optional arguments: --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: --min_seq INT Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100) --motif_min_key INT Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8) @@ -89,12 +92,12 @@ Optional arguments: --iteration INT Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000) --tomtom_treshold float Threshold for similarity score. (Default: 0.01) --best_motif INT Get the best X motifs per cluster. (Default: 3) - + Moitf clustering: --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0) --edge_weight INT Minimum weight of edges in motif-cluster-graph (Default: 5) --motif_similarity_thresh FLOAT Threshold for motif similarity score (Default: 0.00001) - + Creating GTF: --organism [hg38 | hg19 | mm9 | mm10] Input organism --tissues List/String List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON