From bd2e900e69eb4fc28ee1963a2ac65b1e7fad046e Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Fri, 18 Dec 2020 10:25:25 +0100
Subject: [PATCH] add rule for strainphlan
---
tools/strainphlan/sample2markers/README.md | 3 +++
tools/strainphlan/strainphlan/Snakefile | 25 ++++++++++++++++++++++
tools/strainphlan/strainphlan/config.yaml | 5 +++++
3 files changed, 33 insertions(+)
create mode 100644 tools/strainphlan/strainphlan/Snakefile
create mode 100644 tools/strainphlan/strainphlan/config.yaml
diff --git a/tools/strainphlan/sample2markers/README.md b/tools/strainphlan/sample2markers/README.md
index 8ef1f3b..78053e7 100644
--- a/tools/strainphlan/sample2markers/README.md
+++ b/tools/strainphlan/sample2markers/README.md
@@ -2,6 +2,9 @@
This step will reconstruct all species strains found in metaphlan output sam file and store them in a pickle file (*.pkl). Those strains are referred as sample-reconstructed strains.
+.. **Note**: output pkl file is written should be written in a individual directory since the script tries
+ to create and write into a `tmp` dir that leads to error when running sample2markers.py in parallel.
+
### Help section
```
diff --git a/tools/strainphlan/strainphlan/Snakefile b/tools/strainphlan/strainphlan/Snakefile
new file mode 100644
index 0000000..bf6d4ef
--- /dev/null
+++ b/tools/strainphlan/strainphlan/Snakefile
@@ -0,0 +1,25 @@
+__strainphlan_exec_command = config.get('strainphlan', {}).get('exec_command', 'strainphlan')
+__strainphlan_modules = config.get('strainphlan', {}).get('modules')
+__strainphlan_options = config.get('strainphlan', {}).get('options', "")
+__strainphlan_threads = config.get('strainphlan', {}).get('threads', 1)
+
+
+rule strainphlan:
+ input:
+ __strainphlan_input
+ output:
+ __strainphlan_output
+ params:
+ exec_command = __strainphlan_exec_command,
+ modules = __strainphlan_modules,
+ clade = __strainphlan_clade,
+ output_dir = __strainphlan_output_dir,
+ options = __strainphlan_options
+ threads:
+ __strainphlan_threads
+ run:
+ command = []
+ if params.modules:
+ command.append("module load {params.modules}")
+ command.append("{params.exec_command} -s {input} -n {threads} -c {params.clade} {params.options} -o {params.output_dir}")
+ shell(" && ".join(command))
diff --git a/tools/strainphlan/strainphlan/config.yaml b/tools/strainphlan/strainphlan/config.yaml
new file mode 100644
index 0000000..9094c16
--- /dev/null
+++ b/tools/strainphlan/strainphlan/config.yaml
@@ -0,0 +1,5 @@
+input_dir: data
+
+strainphlan:
+ threads: 4
+ exec_command: sample2markers.py
--
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