From 1c6bcf120bdd0832d6df3061584031cf4b3a16b2 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Thu, 20 Dec 2018 14:52:37 +0100 Subject: [PATCH 1/2] Added new parameter list to README.mf --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 41ee001..d139f97 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ For further information read the [documentation](https://github.molgen.mpg.de/lo ## Installation Start with installing all dependencies listed above (Nextflow, conda) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018). -Every other dependency will be automatically installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run. +Every other dependency will be automatically installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run. It is **not** required to create and activate the enviroment from the yaml-file beforehand. **Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two differnt packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfisch package from the channel conda-forge! @@ -30,14 +30,16 @@ Required arguments: --genome_fasta Path to genome in FASTA-format --motif_db Path to motif-database in MEME-format --config Path to UROPA configuration file - --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. - Path can be set as tfbs_path in next run. (Default: './') - --out Output Directory (Default: './out/') - + --organism Input organism [hg38 | hg19 | mm9 | mm10] + --out Output Directory (Default: './out/') + Optional arguments: - + --help [0|1] 1 to show this help message. (Default: 0) --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. + --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. + Path can be set as tfbs_path in next run. (Default: './') + --gtf_path Path to gtf-file. If path is set the process which creats a gtf-file is skipped. Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) @@ -77,7 +79,6 @@ Optional arguments: --motif_similarity_thresh FLOAT Threshold for motif similarity score (Default: 0.00001) Creating GTF: - --organism [hg38 | hg19 | mm9 | mm10] Input organism --tissues List/String List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON config All arguments can be set in the configuration files @@ -103,4 +104,3 @@ path=[Path to given masterenv.yml file] conda env create --name masterenv -f $path ``` When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it. - From 13bccdafbb5ab5d4c8f2e43304167ad564a50106 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Fri, 21 Dec 2018 06:46:11 -0500 Subject: [PATCH 2/2] Fixed bug in pipeline.nf: parameter gtf_path is now working --- pipeline.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 1be18be..f5f709c 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -9,7 +9,7 @@ params.tfbs_path="" params.create_known_tfbs_path = "./" params.help = 0 - params.get_path="" + params.gtf_path="" params.out = "./out/" //peak_calling @@ -583,7 +583,7 @@ process create_GTF { file ('*.gtf') into gtf when: - gtf_path == "" + params.gtf_path == "" script: """ @@ -591,7 +591,7 @@ process create_GTF { """ } -if (gtf_path == "") { +if (params.gtf_path == "") { gtf_for_uropa = gtf } else { gtf_for_uropa = Channel.fromPath(params.gtf_path)