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0f88bad
Update parameter names in create_gtf.config
renewiegandt Jan 23, 2019
4bef518
Update parameter names in footprint_extraction.config
renewiegandt Jan 23, 2019
0f0aa58
Update parameter names in moitif_estimation.config
renewiegandt Jan 23, 2019
7e90339
pipeline.nf: Added check for unknown parameters; update parameter nam…
renewiegandt Jan 23, 2019
e2494a0
Removed debugging code
renewiegandt Jan 23, 2019
987bf7f
Merge pull request #91 from loosolab/estimation_motifs
renewiegandt Jan 23, 2019
170ca1e
get_motif_seq.R: Removed redundant code
renewiegandt Jan 28, 2019
565d4b8
Rename get_motif_seq.R
renewiegandt Jan 28, 2019
e470bed
pipeline.nf: changed output dir of logs
renewiegandt Jan 28, 2019
b931ea7
compareBed.sh: rename stats to log
renewiegandt Jan 28, 2019
35d6f0c
Added venn.R to 3.2_evaluation
renewiegandt Feb 4, 2019
98654e1
Update uropa.config
renewiegandt Feb 4, 2019
2186cc6
Added uropa to the enviroment yaml
renewiegandt Feb 4, 2019
3793c70
Added uropa and venn process; mergeing gtf files; added parameter for…
renewiegandt Feb 4, 2019
1a95d4c
Added yaml-file for meme-suite enviroment
renewiegandt Feb 11, 2019
011b99a
Added meme_env parameter
renewiegandt Feb 11, 2019
10a3df3
Fixed channel for venn; added conda meme-env
renewiegandt Feb 11, 2019
4c08eeb
added parameter gap penalty to 2.2config
renewiegandt Feb 11, 2019
9bf3ed9
merge_similar_clusters.R: bugfix
renewiegandt Feb 11, 2019
50ec488
fixed label_cluster; minor changes
renewiegandt Feb 11, 2019
e11e0af
merge_similar_clusters: bugfix; improved cluster plot
renewiegandt Mar 4, 2019
a46476f
pipeline: added uropa summary to output
renewiegandt Mar 4, 2019
51dcfc0
merge_similar_clusters: fixed filenames
renewiegandt Mar 4, 2019
f1eb5f1
pipeline: Added seed for glam2
renewiegandt Mar 4, 2019
c034878
Added skript png_to_pdf
renewiegandt Mar 20, 2019
fae46c6
Better output directory names
renewiegandt Mar 20, 2019
cdc73a2
Minor formating changes of output file
renewiegandt Mar 20, 2019
89ae057
Update parameters in README
renewiegandt Mar 26, 2019
f8c572b
Added new parameters to config files
renewiegandt Mar 26, 2019
5d9fb6c
Minor changes
renewiegandt Mar 26, 2019
07d492c
Minor changes
renewiegandt Mar 26, 2019
d6b44ea
Merge pull request #92 from loosolab/estimation_motifs
renewiegandt Mar 26, 2019
183483f
Renamed log file
renewiegandt Mar 28, 2019
9b5cd47
Update: new parameters
renewiegandt Mar 28, 2019
bce6e1b
sorting gtf; bug fix; renaming gtf parameter
renewiegandt Mar 28, 2019
8f9fbee
Merge pull request #93 from loosolab/estimation_motifs
renewiegandt Mar 28, 2019
2e14753
Added TODO
renewiegandt Apr 5, 2019
5caf87e
Update test run
renewiegandt Apr 12, 2019
f210c5e
Improved error handling if parameter is missing
renewiegandt Apr 12, 2019
66c11ff
Merge branch 'dev' into estimation_motifs
renewiegandt Apr 12, 2019
3caf997
Added error message for missing required parameters
renewiegandt Apr 16, 2019
1b4d9c3
Reworked check on required parameters
renewiegandt Apr 16, 2019
a58cc18
Merge pull request #95 from loosolab/estimation_motifs
renewiegandt Apr 16, 2019
8069aba
Added nextflwo to masterenv.yml
renewiegandt Apr 16, 2019
3ef6756
Merge pull request #96 from loosolab/estimation_motifs
renewiegandt Apr 16, 2019
f7da052
Add fixed channel for jellyfish package
renewiegandt Apr 16, 2019
99cefb6
Update documentation for installation
renewiegandt Apr 16, 2019
a3f074c
Merge pull request #97 from loosolab/estimation_motifs
renewiegandt Apr 16, 2019
bc25457
Update README.md
renewiegandt Apr 16, 2019
a36e060
Update README.md
renewiegandt Apr 16, 2019
db3c470
Update README.md
renewiegandt Apr 16, 2019
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pipeline.nf: Added check for unknown parameters; update parameter nam…
…es; if compareBed.sh is not executable chmod +x is called
renewiegandt committed Jan 23, 2019
commit 7e90339659d092bfafb642dd5aed06c4d8ba3da9
26 changes: 22 additions & 4 deletions pipeline.nf
Original file line number Diff line number Diff line change
@@ -35,7 +35,7 @@
params.identity=0.8
params.sequence_coverage=8
params.memory=800
params.throw_away_seq=9
params.throw_away_seq=9
params.strand=0

//motif_estimation
@@ -60,7 +60,7 @@

//creating_gtf
params.organism=""
params.tissue=""
params.tissues=""

if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0" ){
log.info """
@@ -144,20 +144,27 @@ int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer",
"aprox_motif_len", "motif_occurence", "min_seq_length", "global",
"sequence_coverage", "memory", "throw_away_seq", "strand",
"min_seq", "motif_min_key", "motif_max_key", "iteration",
"edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight"]
"edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight",
"threads", ]
req_params = ["bigwig", "bed", "genome_fasta", "motif_db", "config"]
all_params = int_params + req_params + ["organism" , "identity", "tfbsscan_method",
"percentage", "tomtom_treshold", "motif_similarity_thresh", "out",
"tissues", "gtf_path", "cluster_motif", "tfbs_path", "help"]

valid_organism = ["hg38", "hg19", "mm9", "mm10"]
valid_tfbsscan_methods = ["moods","fimo"]

params.each { key, value ->
if (!(all_params.contains(key))){
println("Warning: Parameter $key is unknown. Please check for typos or the parameter list!")
}
if(int_params.contains(key)) {
if (!("${value}" ==~ /\d+/ )){
println("ERROR: $key needs to be an Integer")
System.exit(2)
}
}
if(req_params.contains(key)) {
if(req_params.contains(key) || (key == "gtf_path" && value != "") ) {
if(!file(value).exists()) {
println("ERROR: $key not found. Please check the given path.")
System.exit(2)
@@ -243,12 +250,20 @@ process overlap_with_known_TFBS {
script:
if(params.tfbs_path == ""){
"""
if [[ ! -x "${path_bin}/1.2_filter_motifs/compareBed.sh" ]]
then
chmod +x ${path_bin}/1.2_filter_motifs/compareBed.sh
fi
python ${path_bin}/1.2_filter_motifs/tfbsscan.py --use ${params.tfbsscan_method} --core ${params.threads} -m ${db} -g ${fasta} -o ./known_tfbs -b ${bed_peaks}
${path_bin}/1.2_filter_motifs/compareBed.sh --data ${bed_footprints} --motifs ./known_tfbs --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp}
cp -r ./known_tfbs/ ${params.out}/1.2_filter_motifs/
"""
} else {
"""
if [[ ! -x "${path_bin}/1.2_filter_motifs/compareBed.sh" ]]
then
chmod +x ${path_bin}/1.2_filter_motifs/compareBed.sh
fi
${path_bin}/1.2_filter_motifs/compareBed.sh --data ${bed_footprints} --motifs ${known_tfbs} --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp}
"""
}
@@ -274,6 +289,9 @@ process reduce_sequence {
set name, file ('*.bed') into bed_for_clustering
file ('*.log')

when:
params.lalal == "1"

script:
"""
Rscript ${path_bin}/2.1_clustering/reduce_sequence.R -i ${bed} -k ${params.kmer} -m ${params.aprox_motif_len} -o ${name}_reduced.bed -t ${params.threads} -f ${params.motif_occurence} -s ${params.min_seq_length} --summary reduce_sequence.log