minor changes

masterenv.yml

@@ -5,11 +5,9 @@ channels:
   - conda-forge
 dependencies:
   - bedtools
-  - python
   - r-seqinr
   - numpy
   - pybigWig
-  #clustering
   - cd-hit
   - jellyfish
   - r-base>=3.5.1
@@ -20,11 +18,10 @@ dependencies:
   - r-stringr
   - r-optparse
   - bioconductor-iranges
-#
   - snakemake
   - meme
   - moods
   - biopython
   - pybedtools
   - matplotlib
-  - seaborn
+  - seaborn

nextflow.config

@@ -1,14 +1,15 @@
+wd = "/mnt/agnerds/Rene.Wiegandt/10_Master/masterJLU2018"
 createTimeout = 60
 params.threads=1 //Parameter for for scripts! Not for nextflow processes.
-params.config="${workflow.projectDir}/config/uropa.config"
-
-includeConfig '$workflow.projectDir/config/peak_calling.config'
-includeConfig '$workflow.projectDir/config/filter_unknown_motifs.config'
-includeConfig '$workflow.projectDir/config/cluster.config'
-includeConfig '$workflow.projectDir/config/motif_estimation.config'
-includeConfig '$workflow.projectDir/config/create_gtf.config'
+params.config="${wd}/config/uropa.config"
 
 env {
-	path_bin = $workflow.projectDir/bin
-	path_env = $workflow.projectDir/masterenv.yml
+	path_bin = "${wd}/bin"
+	path_env = "${wd}/masterenv.yml"
 }
+
+includeConfig "${wd}/config/peak_calling.config"
+includeConfig "${wd}/config/filter_unknown_motifs.config"
+includeConfig "${wd}/config/cluster.config"
+includeConfig "${wd}/config/motif_estimation.config"
+includeConfig "${wd}/config/create_gtf.config"

pipeline.nf

@@ -86,9 +86,10 @@ All arguments can be set in the configuration files.
 }
 
 
-bigwig_input.combine(bed_input).set{footprint_in}
-
+bigwig_input.combine(bed_input).into {footprint_in}
+/*
 
+*/
 process footprint_extraction {
 	conda "${path_env}"
 
@@ -103,12 +104,16 @@ process footprint_extraction {
 	set name, file ('*.bed') into bed_for_overlap_with_TFBS
 
 	script:
+	print(bigWig)
 	"""
 	python ${path_bin}/call_peaks.py --bigwig ${bigWig} --bed ${bed} --output_file ${name}_called_peaks.bed --window_length ${params.window_length} --step ${params.step} --percentage ${params.percentage}
 	"""
 }
 
 //Abfrage ob ausgeführt werden muss.
+/*
+
+*/
 process extract_known_TFBS {
 	conda "${path_env}"
 
@@ -129,6 +134,8 @@ process extract_known_TFBS {
 bed_for_overlap_with_TFBS.combine(known_TFBS_for_overlap).combine(fa_overlap_2).set {for_overlap}
 
 
+/*
+*/
 process overlap_with_known_TFBS {
 	conda "${path_env}"
 
@@ -146,6 +153,8 @@ process overlap_with_known_TFBS {
 }
 
 
+/*
+*/
 process reduce_bed {
 	conda "${path_env}"
 
@@ -162,6 +171,8 @@ process reduce_bed {
 }
 
 
+/*
+*/
 process clustering {
 	conda "${path_env}"
 
@@ -178,7 +189,9 @@ process clustering {
 }
 
 
-// Converting BED-File to one FASTA-File per cluster
+/*
+Converting BED-File to one FASTA-File per cluster
+*/
 process bed_to_clustered_fasta {
 		conda "${path_env}"
 
@@ -202,8 +215,10 @@ process bed_to_clustered_fasta {
 fasta_for_glam2 = fasta_for_glam2.flatten().map {it -> [it.simpleName, it]}
 
 
-//Running GLAM2 on FASTA-files.
-//Generating Motifs through alignment and scoring best local matches.
+/*
+Running GLAM2 on FASTA-files.
+Generating Motifs through alignment and scoring best local matches.
+*/
 process glam2 {
 		conda "${path_env}"
 
@@ -221,9 +236,10 @@ process glam2 {
     """
 }
 
-
-//Running Tomtom on meme-files generated by GLAM2.
-//Tomtom searches motifs in databases.
+/*
+Running Tomtom on meme-files generated by GLAM2.
+Tomtom searches motifs in databases.
+*/
 process tomtom {
 		conda "${path_env}"