From a37db2548568ae8a33107439fcff5f75090bea88 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 15:14:54 +0100
Subject: [PATCH] Add raw indexing
---
raw_inputs/raw_accel_align_index.py | 14 ++++
raw_inputs/raw_accel_align_index.yaml | 13 ++++
.../accel_align_index.rule.snakefile | 18 +++++
.../accel_align_index/accel_align_index.yaml | 71 +++++++++++++++++++
tools/global.yaml | 1 +
5 files changed, 117 insertions(+)
create mode 100755 raw_inputs/raw_accel_align_index.py
create mode 100755 raw_inputs/raw_accel_align_index.yaml
create mode 100755 tools/accel_align_index/accel_align_index.rule.snakefile
create mode 100755 tools/accel_align_index/accel_align_index.yaml
diff --git a/raw_inputs/raw_accel_align_index.py b/raw_inputs/raw_accel_align_index.py
new file mode 100755
index 00000000..c3e34f56
--- /dev/null
+++ b/raw_inputs/raw_accel_align_index.py
@@ -0,0 +1,14 @@
+import os
+import re
+import sys
+
+def raw_accel_align_index(results_dir, accel_align_index):
+ out = dict()
+ from os import listdir
+ from os.path import isfile, join
+ onlyfiles = [join(accel_align_index, f) for f in listdir(accel_align_index) if isfile(join(accel_align_index, f))]
+ out["accel_align_index"] = onlyfiles
+
+ return(out)
+
+#print(raw_accel_align_index(sys.argv[1],sys.argv[2]) )
\ No newline at end of file
diff --git a/raw_inputs/raw_accel_align_index.yaml b/raw_inputs/raw_accel_align_index.yaml
new file mode 100755
index 00000000..5582b49a
--- /dev/null
+++ b/raw_inputs/raw_accel_align_index.yaml
@@ -0,0 +1,13 @@
+{
+ name: raw_accel_align_index,
+ function_call: "raw_accel_align_index(config['results_dir'], config['accel_align_index'])",
+ options: [
+ {
+ name: "accel_align_index",
+ type: "input_dir",
+ value: "/Data",
+ label: "Directory containing the Accel-Align index files: ",
+ volumes: [Data: "/Data", Results: "/Results"]
+ }
+ ]
+}
\ No newline at end of file
diff --git a/tools/accel_align_index/accel_align_index.rule.snakefile b/tools/accel_align_index/accel_align_index.rule.snakefile
new file mode 100755
index 00000000..46e2bf17
--- /dev/null
+++ b/tools/accel_align_index/accel_align_index.rule.snakefile
@@ -0,0 +1,18 @@
+rule <step_name>__accel_align_index:
+ input:
+ **<step_name>__accel_align_index_inputs()
+ output:
+ index = config["<step_name>__accel_align_index_output_dir"]+"/index.hash",
+ log:
+ config["results_dir"]+"/logs/" + config["<step_name>__accel_align_index_output_dir"] + "/index.log"
+ params:
+ command = config["<step_name>__accel_align_index_command"],
+ accel_align_index_kmers_length = config["<step_name>__accel_align_index_kmers_length"],
+ out_dir = config["<step_name>__accel_align_index_output_dir"]
+ shell:
+ "{params.command} "
+ "-l {params.accel_align_index_kmers_length} "
+ "{input.genome_fasta} "
+ "|& tee {log};"
+ "cp {input.genome_fasta} {params.out_dir}/index "
+ "cp {input.genome_fasta}.hash {params.out_dir}/index.hash "
diff --git a/tools/accel_align_index/accel_align_index.yaml b/tools/accel_align_index/accel_align_index.yaml
new file mode 100755
index 00000000..4633b078
--- /dev/null
+++ b/tools/accel_align_index/accel_align_index.yaml
@@ -0,0 +1,71 @@
+{
+ id: accel_align_index,
+ id: accel_align_index ,
+ name: Accel-align is a fast alignment tool implemented in C++,
+ article: 10.1186/s12859-021-04162-z,
+ website: "https://github.com/raja-appuswamy/accel-align-release",
+ git: "https://github.com/raja-appuswamy/accel-align-release",
+ description: "a fast sequence mapper and aligner based on the seed-embed-extend method",
+ version: "2.0",
+ documentation: "https://github.com/raja-appuswamy/accel-align-release",
+ multiqc: "custom",
+ commands:
+ [
+ {
+ name: accel_align_index,
+ cname: "Bowtie index",
+ command: accindex-x86-64,
+ category: "indexing",
+ output_dir: accel_align/index,
+ inputs: [{ name: genome_fasta, type: "contigs", description: "Fasta reference", from: "parameter" }],
+ outputs: [{ name: index, type: "accel_align_index", file: index, description: "Index files for Accel-Align alignment" }],
+ options:
+ [
+ {
+ name: accel_align_index_genome_fasta,
+ type: input_file,
+ value: "",
+ label: "Path to reference genome fasta file",
+ },
+ {
+ name: accel_align_index_kmers_length,
+ prefix: -l,
+ type: numeric,
+ value: 32,
+ min: 1,
+ max: 64,
+ step: 1,
+ label: "the length of k-mers to use to index genome",
+ }
+ ]
+ },
+ ],
+ install: {
+ accel_align: [
+ "cd /opt/biotools",
+ "git clone https://github.com/raja-appuswamy/accel-align-release.git",
+ "ENV PATH /opt/biotools/accel-align-release:$PATH",
+ ],
+ Intel_TBB: [
+ "apt-get install -y libtbb-dev",
+ ],
+ samtools: [
+ "cd /opt/biotools",
+ "wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2",
+ "tar -xvjf samtools-1.9.tar.bz2",
+ "cd samtools-1.9",
+ "./configure && make",
+ "cd ..",
+ "mv samtools-1.9/samtools bin/samtools",
+ "rm -r samtools-1.9 samtools-1.9.tar.bz2"
+ ]
+ },
+ citations: {
+ accel_align: [
+ "Yan, Y., Chaturvedi, N. & Appuswamy, R. Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method. BMC Bioinformatics 22, 257 (2021)."
+ ],
+ samtools: [
+ "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
+ ]
+ }
+}
\ No newline at end of file
diff --git a/tools/global.yaml b/tools/global.yaml
index cb534829..3e3ea8e4 100755
--- a/tools/global.yaml
+++ b/tools/global.yaml
@@ -53,6 +53,7 @@ data: [
{name: "fast5_dir", category: "sequences"},
{name: "illumina_dir", category: "sequences"},
+ {name: "accel_align_index", category: "index"},
{name: "bowtie_index", category: "index"},
{name: "bowtie2_index", category: "index"},
{name: "bwa_mem_index", category: "index"},
--
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