From 8cf92a293ea84a398a588d7d0bfe114348aad77b Mon Sep 17 00:00:00 2001 From: Jacob Morrison Date: Mon, 8 Jan 2024 14:15:25 -0500 Subject: [PATCH] fix snakemake pipeline table --- docs/snakemake_pipeline.md | 44 +++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/docs/snakemake_pipeline.md b/docs/snakemake_pipeline.md index 36aae71..b3c8e3a 100644 --- a/docs/snakemake_pipeline.md +++ b/docs/snakemake_pipeline.md @@ -11,28 +11,28 @@ analyses. ## Dependencies The following dependencies are downloaded when running with `--use-conda`, otherwise you must have these in your PATH. -| Package | Conda Version Downloaded | Notes | -|:---------------|:------------------------:|:------| -| `snakemake` | 7.0+ | Needed before running pipeline | -| `biscuit` | 1.2.0 | | -| `htslib` | 1.17 | | -| `samtools` | 1.17 | | -| `dupsifter` | 1.2.0 | | -| `parallel` | 20230322 | | -| `bedtools` | 2.30.0 | | -| `preseq` | 3.2.0 | Must be compiled with htslib enabled | -| `fastqc` | 0.12.1 | | -| `trim_galore` | 0.6.10 | | -| `fastq_screen` | 0.15.3 | Only required if running `fastq_screen`) -| `bismark` | 0.24.0 | Only required if running `fastq_screen`) -| `pigz` | 2.6 | | -| `python` | 3.11.3 | | -| `pandas` | 2.0.0 | | -| `numpy` | 1.24.2 | | -| `matplotlib` | 3.7.1 | | -| `seaborn` | 0.12.2 | | -| `multiqc` | 1.14 | | -| `R` | 4.2.3 | | +| Package | Conda Version Downloaded | Notes | +|:---------------|:------------------------:|:------------------------------------------------| +| `snakemake` | 7.0+ | Needed before running pipeline | +| `biscuit` | 1.2.0 | | +| `htslib` | 1.17 | | +| `samtools` | 1.17 | | +| `dupsifter` | 1.2.0 | | +| `parallel` | 20230322 | | +| `bedtools` | 2.30.0 | | +| `preseq` | 3.2.0 | Must be compiled with htslib enabled | +| `fastqc` | 0.12.1 | | +| `trim_galore` | 0.6.10 | | +| `fastq_screen` | 0.15.3 | Only required if running `fastq_screen`) | +| `bismark` | 0.24.0 | Only required if running `fastq_screen`) | +| `pigz` | 2.6 | | +| `python` | 3.11.3 | | +| `pandas` | 2.0.0 | | +| `numpy` | 1.24.2 | | +| `matplotlib` | 3.7.1 | | +| `seaborn` | 0.12.2 | | +| `multiqc` | 1.14 | | +| `R` | 4.2.3 | | | `tidyverse` | 2.0.0 | Only required for plotting methylation controls | | `ggplot2` | 3.4.2 | Only required for plotting methylation controls | | `patchwork` | 1.1.2 | Only required for plotting methylation controls |