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Commits (2)
......@@ -62,7 +62,7 @@ rule report_pipeline:
genes_rubic="Reports/Genes_RUBIC.txt",
venn="Reports/Venn_overlap_genes.png",
swarmplot="Reports/Comparison_sizes.png",
circos="Circos/RecurrentRegions_legend.png",
#FIXME circos="Circos/RecurrentRegions_legend.png",
go="GO/comparison.txt"
output:
html="PipelineResults.html"
......@@ -76,7 +76,7 @@ rule report_pipeline:
- Report on segmentation file: seg_
- Report on comparison between tools and overlapping regions: tools_
- Table with all recurrent regions and overlapping genes: table_regions_
- Circos plot showing the raw segmentation file and recurrent regions detected by both tools: circos_
#FIXME - Circos plot showing the raw segmentation file and recurrent regions detected by both tools: circos_
- Venn diagram showing the overlap between gene lists from both tools: venn_
- Boxplot showing the differences in sizes between both tools: swarmplot_
......
......@@ -2,8 +2,8 @@
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir: /home/beatrice/CNA_99_genegistic
gisticdir: /home/beatrice/CNA_analysis/run_gistic2
workdir: /exports/sasc/hmei/test_CNV #directory to write output
gisticdir: /exports/sasc/hmei/GISTIC2 #directory to install GISTIC2
#Input details to download from firehose
cancer_type: SKCM
......
channels:
- bioconda
dependencies:
- circos =0.69.6
- circos =0.69.2
......@@ -2,9 +2,13 @@ channels:
- conda-forge
- edurand
- bioconda
- pypi
dependencies:
- python =3.6
- python-drmaa
- snakemake =4.5.0
- matplotlib-venn =0.11.5
- matplotlib =2.1.0
- pyensembl =1.1.0
- seaborn =0.8.1
- pillow =5.0.0
......@@ -11,6 +11,8 @@ rule do_GO_analysis:
gene_ID_to_GO=os.path.join(workflow.basedir, config["ID_to_GO"]) if config["ID_to_GO"].startswith("input_files") else config["ID_to_GO"]
benchmark:
"Benchmarks/topGO." + str(datetime.datetime.now()).replace(" ", "_") + ".txt"
resources:
mem_mb=50000
wrapper:
"file:" + workflow.basedir + "/wrappers/topgo"
......
......@@ -2,12 +2,12 @@
#$ -S /bin/bash
#$ -q all.q
#$ -N prioritization
#$ -l h_vmem=20G
#$ -l h_vmem=50G
#$ -cwd
#$ -j Y
#$ -V
#$ -m be
#$ -M b.f.tan@lumc.nl
#$ -M h.mei@lumc.nl
##Create or update conda environment and activate it
conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml &&
......@@ -18,8 +18,10 @@ snakemake -p \
--configfile config.yaml \
--snakefile Snakefile \
--latency-wait 90 \
--jobs 1 \
--jobs 10 \
--drmaa " -N preprocessor -q all.q -cwd -V" \
--drmaa-log-dir $(pwd)/.cluster_logs \
--max-jobs-per-second 10 \
--restart-times 3
# --use-conda \
# --conda-prefix ~/.conda
--restart-times 3 \
--use-conda \
--conda-prefix /exports/sasc/hmei/miniconda2/