From 24ae24b5374a43da55189405f332c6dec9f88f2b Mon Sep 17 00:00:00 2001
From: r1cheu <chenrulei@cemps.ac.cn>
Date: Wed, 20 Mar 2024 14:52:39 +0800
Subject: [PATCH] update README

---
 README.md                  | 11 +++++++++++
 workflow/rules/mapping.smk |  2 ++
 2 files changed, 13 insertions(+)

diff --git a/README.md b/README.md
index 1f3f6bc..dd09841 100644
--- a/README.md
+++ b/README.md
@@ -26,3 +26,14 @@ sudo singularity build snp_gatk.sif snp_call.def
 ### we alse provide a pre-built singularity image
 ```
 
+### Prepare Samples
+modify config/samples.tsv and config/units.tsv.
+
+### Modify the config file
+modify the config/config.yaml file to fit your needs.
+e.g. sif: /path/to/snp_gatk.sif
+### Run the workflow
+
+```bash
+snakemake --profile cluster --cache
+```
\ No newline at end of file
diff --git a/workflow/rules/mapping.smk b/workflow/rules/mapping.smk
index 65a3264..51565ec 100644
--- a/workflow/rules/mapping.smk
+++ b/workflow/rules/mapping.smk
@@ -10,6 +10,7 @@ rule fastp_trim_reads_pe:
         html="logs/fastp/{sample}.html", json="logs/fastp/{sample}.json"
     resources:
         ntasks=4
+        mem_mb=
     shell:
         "fastp -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} "
         "-h {log.html} -j {log.json} -w {resources.ntasks}"
@@ -29,6 +30,7 @@ rule map_reads:
         sort_order="coordinate",
     resources:
         ntasks=4
+        mem_mb=
     shell:
         "bwa mem -t {resources.ntasks} {params.extra} {params.index} {input.reads} | "
         "samtools sort -T {output}.tmp -o {output} - > {log} 2>&1"