diff --git a/README.md b/README.md index ec8e8c7908178f3db77dfc753fec25b483d65a50..bdd7b7cf44b37d47272ec72165634702478fe40e 100644 --- a/README.md +++ b/README.md @@ -73,6 +73,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git 9. Annotate all peaks using ChipSeeker 10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment) 11. Use MEME-ChIP to find motifs in original peaks + 12. Plot enrichment of signal around TSS See [FLOWCHART](docs/flowchart.pdf) diff --git a/docs/index.md b/docs/index.md index 3b4a685cfc112291a221c04d7efa4fb85db9545a..e4e3e018513597745e2b2944e42d2ef05ac02277 100644 --- a/docs/index.md +++ b/docs/index.md @@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste 9. Annotate all peaks using ChipSeeker 10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment) 11. Use MEME-ChIP to find motifs in original peaks + 12. Plot enrichment of signal around TSS ## Workflow Parameters diff --git a/workflow/main.nf b/workflow/main.nf index cb8b1e61cecd3a141da26df31c1b6b06fe38177b..90f0c9076a1e1b436285cb87a3791db520dc8fb7 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -488,6 +488,7 @@ process plotProfile { output: file '*.{png,gz}' into plotProfile + file gtf from gtfFile when: