From 0874a7c72afa7f54ab294464d9cf0b471095cfe4 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:02:12 +0200 Subject: [PATCH 1/6] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ce23475..edfd9e4 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ Note: Green shows a value higher than the scale. ## Installation and Command-line usage ### Dependencies * Linux -* Nextflow version 0.30 +* Nextflow version >= 0.30 * R version version 3.4.4 * ggplot2 * plyr @@ -48,9 +48,9 @@ Note: Green shows a value higher than the scale. * HiCExplorer version 2.1 * Conda: * bowtie2 version 2.3.3.1* - * bwa version 0.7* + * bwa version 0.7.15* * SAMtools version 1.3.1* - * BEDtools version 2.27* + * BEDtools version 2.27.1* * uropa version 2.0.2 alpha* ``* Will be implemented automatically through conda enviroment.`` From 3eae4053df6e4db139fd8276a99ca25bd47fe425 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:05:21 +0200 Subject: [PATCH 2/6] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index edfd9e4..635d664 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,6 @@ Note: Green shows a value higher than the scale. * R version version 3.4.4 * ggplot2 * plyr - * grid * gridExtra * gtable * RColorBrewer From bc4e33a7d7d24988660330d400a93b61b2bb55f1 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:06:41 +0200 Subject: [PATCH 3/6] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 635d664..afba48d 100644 --- a/README.md +++ b/README.md @@ -91,6 +91,7 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi --score_min [INT] - Score range: minimum. [default: 0] --score_max [INT] - Score range: maximium. [default: autoscale] --pn [STRING] - Name of the Project [default: 'Project'] + --organsim [mm10,mm9,hg19] - Type of the genome --mode uropa - Uropa annoation [T2C] parameters: @@ -111,6 +112,7 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi --score_min [INT] - Score range: minimum. [default: 0] --score_max [INT] - Score range: maximium. [default: autoscale] --pn [STRING] - Name of the Project [default: 'Project'] + --organsim [mm10,mm9,hg19] - Type of the genome --mode HiC - Full HiC analysis parameters: From ba7bebf9ec8869ae9bcdc847e07606990b04cbc4 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:07:12 +0200 Subject: [PATCH 4/6] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index afba48d..f81bab4 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi --score_min [INT] - Score range: minimum. [default: 0] --score_max [INT] - Score range: maximium. [default: autoscale] --pn [STRING] - Name of the Project [default: 'Project'] - --organsim [mm10,mm9,hg19] - Type of the genome + --organsim [mm10,mm9,hg19] - Type of the genome --mode uropa - Uropa annoation [T2C] parameters: @@ -112,7 +112,7 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi --score_min [INT] - Score range: minimum. [default: 0] --score_max [INT] - Score range: maximium. [default: autoscale] --pn [STRING] - Name of the Project [default: 'Project'] - --organsim [mm10,mm9,hg19] - Type of the genome + --organsim [mm10,mm9,hg19] - Type of the genome --mode HiC - Full HiC analysis parameters: From 82ce9014781231ae8541108b14cc83b5f93f8006 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:16:27 +0200 Subject: [PATCH 5/6] Update nextflow.config --- nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 03f9dd4..22bebea 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,8 +4,8 @@ env { path_python = "/mnt/software/x86_64/packages/python/2.7.8-anaconda-5.1.0-stretch/bin" //Path to python path_R = "/mnt/software/x86_64/packages/r/3.4.4-stretch-local/bin" //Path to R - path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN" // Path to T2C analysis scripts - path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN" //Path to directory where files are stored. If restriction maps are already existing put them in folder 01_restriction_maps inside this working_dir + path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN" // Path to parent folder containing bin folder with T2C analysis scripts. + path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN" // Working directory. path_genome = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe/index_bwa/GRCm38.p5.genome_whitelist.fa" // Path to full genome in fasta format + basis name of index [e.g. GRCm38.p5.genome_whitelist.fa] path_gtf = "/mnt/agnerds/Rene.Wiegandt/fromMario/gencode.vM15.annotation.gtf" From 6fa758e4927c8840c6d43943374d53dec19f3a7e Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 24 Sep 2018 10:21:49 +0200 Subject: [PATCH 6/6] Update TOuCAN.nf --- TOuCAN.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/TOuCAN.nf b/TOuCAN.nf index a2a346b..ee66864 100644 --- a/TOuCAN.nf +++ b/TOuCAN.nf @@ -9,7 +9,7 @@ params.safe_all_files = 0 params.check_res_maps = 0 params.organism = "mm10" params.pn = "Project" -params.reassin = 0 +params.reassin = 1 // parameter for T2C plots params.chr = ""