From 1a6ce69573c213fad5655810a12eed2b6d43940a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Mon, 19 Nov 2018 04:43:48 -0500 Subject: [PATCH] added script for process 'footprint_extraction' --- pipeline.nf | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 83e4736..dd67c85 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -58,7 +58,7 @@ process overlap_with_known_TFBS { process clustering { input: - file (faste) from FASTA_for_clustering + file (fasta) from FASTA_for_clustering output: set name, file ('*.bed') into bed_for_motif_esitmation @@ -132,7 +132,7 @@ process tomtom { } -//Joining channels with meme and tsv files. Filter joined channel on linecount. +//Joining channels with meme and tsv files. Filter joined channel on line count. //Only meme-files which corresponding tsv files have linecount <= 1 are writen to next channel. for_filter = meme_for_filter.join( tsv_for_filter ) for_filter @@ -143,7 +143,7 @@ for_filter .into { meme_for_scan; check } -//If unknown channel is empty print errormessage +//If channel 'check' is empty print errormessage process check_for_unknown_motifs { echo true @@ -160,6 +160,7 @@ process check_for_unknown_motifs { } +//Get the best(first) Motif from each MEME-file process get_best_motif { input: @@ -220,6 +221,8 @@ process create_GTF { bed_for_final_filter.combine(gtf_for_uropa).set {uropa_in} +// Create configuration file for UROPA. +// Takes template and replaces bed- and gtf-placeholders with actual paths. process create_uropa_config { publishDir '/mnt/agnerds/Rene.Wiegandt/10_Master/', mode: 'copy'