From 8f2f79caade612fd485f6d0fb2b6e051a97a299e Mon Sep 17 00:00:00 2001 From: Zachary Nolen Date: Fri, 22 Mar 2024 17:50:48 +0100 Subject: [PATCH] Fix example config files being swapped --- docs/config.md | 36 +++++++++++++++++++++--------------- mkdocs.yml | 2 ++ 2 files changed, 23 insertions(+), 15 deletions(-) diff --git a/docs/config.md b/docs/config.md index 69f3633..6885474 100644 --- a/docs/config.md +++ b/docs/config.md @@ -13,15 +13,13 @@ running snakemake with `--configfile `. This file contains your sample list, and has four tab separated columns: ``` -sample unit lib platform fq1 fq2 bam sra -hist1 BHVN22DSX2.2 hist1 ILLUMINA data/fastq/hist1.r1.fastq.gz data/fastq/hist1.r2.fastq.gz -hist1 BHVN22DSX2.3 hist1 ILLUMINA data/fastq/hist1.unit2.r1.fastq.gz data/fastq/hist1.unit2.r2.fastq.gz -hist2 BHVN22DSX2.2 hist2 ILLUMINA data/fastq/hist2.r1.fastq.gz data/fastq/hist2.r2.fastq.gz -hist3 BHVN22DSX2.2 hist2 ILLUMINA data/fastq/hist3.r1.fastq.gz data/fastq/hist3.r2.fastq.gz -mod1 AHW5NGDSX2.3 mod1 ILLUMINA data/fastq/mod1.r1.fastq.gz data/fastq/mod1.r2.fastq.gz -mod2 AHW5NGDSX2.3 mod2 ILLUMINA data/bam/mod2.bam -mod3 AHW5NGDSX2.3 mod3 ILLUMINA data/fastq/mod3.r1.fastq.gz data/fastq/mod3.r2.fastq.gz -SAMN13218652 SRR10398077 SAMN13218652 ILLUMINA SRR10398077 +sample population time depth +hist1 Hjelmseryd historical low +hist2 Hjelmseryd historical low +hist3 Hjelmseryd historical low +mod1 Gotafors modern high +mod2 Gotafors modern high +mod3 Gotafors modern high ``` - `sample` contains the ID of a sample. It is best if it only contains @@ -45,7 +43,14 @@ columns: ``` sample unit lib platform fq1 fq2 bam sra -sample1 +hist1 BHVN22DSX2.2 hist1 ILLUMINA data/fastq/hist1.r1.fastq.gz data/fastq/hist1.r2.fastq.gz +hist1 BHVN22DSX2.3 hist1 ILLUMINA data/fastq/hist1.unit2.r1.fastq.gz data/fastq/hist1.unit2.r2.fastq.gz +hist2 BHVN22DSX2.2 hist2 ILLUMINA data/fastq/hist2.r1.fastq.gz data/fastq/hist2.r2.fastq.gz +hist3 BHVN22DSX2.2 hist2 ILLUMINA data/fastq/hist3.r1.fastq.gz data/fastq/hist3.r2.fastq.gz +mod1 AHW5NGDSX2.3 mod1 ILLUMINA data/fastq/mod1.r1.fastq.gz data/fastq/mod1.r2.fastq.gz +mod2 AHW5NGDSX2.3 mod2 ILLUMINA data/bam/mod2.bam +mod3 AHW5NGDSX2.3 mod3 ILLUMINA data/fastq/mod3.r1.fastq.gz data/fastq/mod3.r2.fastq.gz +SAMN13218652 SRR10398077 SAMN13218652 ILLUMINA SRR10398077 ``` - `sample` contains the ID of a sample. Must be same as in `samples.tsv` and @@ -78,11 +83,12 @@ the units file. - `sra` provides the NCBI SRA accession number for a set of paired end fastq files that will be downloaded to be processed. -It is possible to have different samples start from different inputs (i.e. some -from bam, others from fastq, others from SRA). It is best to provide only -`fq1`+`fq2`, `bam`, or `sra` for each sample to be clear where each sample -starts. If multiple are provided for each sample, the bam file will override -fastq or SRA entries, and the fastq will override SRA entries. +!!! note + It is possible to have different samples start from different inputs (i.e. + some from bam, others from fastq, others from SRA). It is best to provide + only `fq1`+`fq2`, `bam`, or `sra` for each sample to be clear where each + sample starts. If multiple are provided for each sample, the bam file will + override fastq or SRA entries, and the fastq will override SRA entries. ## Configuration file diff --git a/mkdocs.yml b/mkdocs.yml index 6186b6c..68f707f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -9,6 +9,8 @@ theme: name: material icon: repo: simple/github + admonition: + note: octicons/tag-16 features: - search.highlight repo_url: https://github.com/zjnolen/angsd-snakemake-pipeline