diff --git a/pipeline.nf b/pipeline.nf index 3d51f1b..1be18be 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -9,6 +9,7 @@ params.tfbs_path="" params.create_known_tfbs_path = "./" params.help = 0 + params.get_path="" params.out = "./out/" //peak_calling @@ -68,8 +69,6 @@ Required arguments: --genome_fasta Path to genome in FASTA-format --motif_db Path to motif-database in MEME-format --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: './') --organism Input organism [hg38 | hg19 | mm9 | mm10] --out Output Directory (Default: './out/') @@ -77,6 +76,9 @@ Optional arguments: --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. + --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: './') + --gtf_path Path to gtf-file. If path is set the process which creats a gtf-file is skipped. Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) @@ -578,7 +580,10 @@ process create_GTF { publishDir "${params.out}/gtf/", mode: 'copy' output: - file ('*.gtf') into gtf_for_uropa + file ('*.gtf') into gtf + + when: + gtf_path == "" script: """ @@ -586,6 +591,12 @@ process create_GTF { """ } +if (gtf_path == "") { + gtf_for_uropa = gtf +} else { + gtf_for_uropa = Channel.fromPath(params.gtf_path) +} + /* bed_for_final_filter.combine(gtf_for_uropa).set {uropa_in}