From 30151f79f9923088c993548b73bd0a3d31fbb9db Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 14:38:30 +0100
Subject: [PATCH] Add Accel-Align mapper
---
tools/accel_align/accel_align.rule.snakefile | 63 ++++++++
tools/accel_align/accel_align.yaml | 144 +++++++++++++++++++
2 files changed, 207 insertions(+)
create mode 100755 tools/accel_align/accel_align.rule.snakefile
create mode 100755 tools/accel_align/accel_align.yaml
diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
new file mode 100755
index 00000000..aec3ef40
--- /dev/null
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -0,0 +1,63 @@
+if config["SeOrPe"] == "PE":
+
+ rule <step_name>__accel_align_PE:
+ input:
+ **<step_name>__accel_align_PE_inputs()
+ output:
+ bam = config["results_dir"]+"/"+config["<step_name>__accel_align_PE_output_dir"]+"/{sample}.bam"
+ log:
+ config["results_dir"]+"/logs/" + config["<step_name>__accel_align_PE_output_dir"] + "/{sample}_accel_align_log.txt"
+ threads:
+ config["<step_name>__accel_align_threads"]
+ params:
+ command = config["<step_name>__accel_align_PE_command"],
+ #indexPrefix = config["<step_name>__accel_align_index_output_dir"]+"/index",
+ #/patho_index/indexName.fna.hash
+ indexPrefix = lambda w, input: os.path.splitext([x for x in input.index ][0])[0],
+ accel_align_seed_length = config["<step_name>__accel_align_seed_length"],
+ accel_align_insert_size = config["<step_name>__accel_align_insert_size"],
+ accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
+ accel_align_alignment_free = "-x" if config["<step_name>__accel_align_alignment_free"] else "",
+ shell:
+ "{params.command} "
+ "-t {threads} "
+ "-l {params.accel_align_seed_length} "
+ "-p {params.accel_align_insert_size} "
+ "{params.accel_align_alignment_free} "
+ "{params.accel_align_alignment_free} "
+ "{params.indexPrefix} "
+ "{input.read} {input.read2} 2> {log} "
+ "| samtools view -b 2>> {log} "
+ "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+ "samtools index -@ {threads} {output.bam} 2>> {log}"
+
+
+elif config["SeOrPe"] == "SE":
+
+ rule <step_name>__accel_align_SE:
+ input:
+ **<step_name>__accel_align_SE_inputs()
+ output:
+ bam = config["results_dir"]+"/"+config["<step_name>__accel_align_SE_output_dir"]+"/{sample}.bam"
+ log:
+ config["results_dir"]+"/logs/" + config["<step_name>__accel_align_SE_output_dir"] + "/{sample}_accel_align_log.txt"
+ threads:
+ config["<step_name>__accel_align_threads"]
+ params:
+ command = config["<step_name>__accel_align_PE_command"],
+ accel_align_seed_length = config["<step_name>__accel_align_seed_length"],
+ accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
+ accel_align_alignment_free = "-x" if config["<step_name>__accel_align_alignment_free"] else "",
+ #indexPrefix = config["<step_name>__accel_align_index_output_dir"]+"/index",
+ indexPrefix = lambda w, input: os.path.splitext([x for x in input.index][0])[0],
+ shell:
+ "{params.command} "
+ "-t {threads} "
+ "-l {params.accel_align_seed_length} "
+ "{params.accel_align_alignment_free} "
+ "{params.accel_align_alignment_free} "
+ "{params.indexPrefix} "
+ "{input.read} 2> {log} "
+ "| samtools view -b 2>> {log} "
+ "| samtools sort -@ {threads} > {output.bam} 2>> {log} &&"
+ "samtools index -@ {threads} {output.bam} 2>> {log}"
diff --git a/tools/accel_align/accel_align.yaml b/tools/accel_align/accel_align.yaml
new file mode 100755
index 00000000..b8e00a58
--- /dev/null
+++ b/tools/accel_align/accel_align.yaml
@@ -0,0 +1,144 @@
+{
+ id: accel_align,
+ 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_PE,
+ cname: "Accel-align PE",
+ command: accalign-x86-64,
+ category: "mapping",
+ output_dir: accel_align/PE,
+ inputs: [{ name: read, type: "reads" }, { name: read2, type: "reads" }, { name: index, type: "accel_align_index", file: index, description: "Index files for accel_align alignment" }],
+ outputs: [{ name: bam, type: "bams", file: "{sample}.bam", description: "Alignment files" }],
+ options:
+ [
+ {
+ name: accel_align_threads,
+ prefix: -t,
+ type: numeric,
+ value: 4,
+ min: 1,
+ max: NA,
+ step: 1,
+ label: "Number of threads to use",
+ },
+ {
+ name: accel_align_seed_length,
+ prefix: -l,
+ type: numeric,
+ value: 32,
+ min: 10,
+ max: 100,
+ step: 1,
+ label: "length of seed",
+ },
+ {
+ name: accel_align_insert_size,
+ prefix: -p,
+ type: numeric,
+ value: 1000,
+ min: 10,
+ max: 400,
+ step: 10,
+ label: "the maximum distance allowed between the paired-end reads (maximum read length supported are 512)",
+ },
+ {
+ name: accel_align_softclipping,
+ prefix: -s,
+ type: checkbox,
+ value: FALSE,
+ label: "Take into account softclipping",
+ },
+ {
+ name: accel_align_alignment_free,
+ prefix: -x,
+ type: checkbox,
+ value: FALSE,
+ label: "alignment-free mapping mode where the position is reported without the CIGAR string",
+ }
+ ]
+ },
+ {
+ name: accel_align_SE,
+ cname: "Accel-align SE",
+ command: accalign-x86-64 ,
+ category: "mapping",
+ output_dir: accel_align/SE,
+ inputs: [{ name: read, type: "reads" }, { name: index, type: "accel_align_index", file: index, description: "Index files for accel_align alignment" }],
+ outputs: [{ name: bam, type: "bams", file: "{sample}.bam", description: "Alignment files" }],
+ options:
+ [
+ {
+ name: accel_align_threads,
+ prefix: -t,
+ type: numeric,
+ value: 4,
+ min: 1,
+ max: NA,
+ step: 1,
+ label: "Number of threads to use",
+ },
+ {
+ name: accel_align_seed_length,
+ prefix: -l,
+ type: numeric,
+ value: 32,
+ min: 10,
+ max: 100,
+ step: 1,
+ label: "length of seed",
+ },
+ {
+ name: accel_align_softclipping,
+ prefix: -s,
+ type: checkbox,
+ value: FALSE,
+ label: "Take into account softclipping",
+ },
+ {
+ name: accel_align_alignment_free,
+ prefix: -x,
+ type: checkbox,
+ value: FALSE,
+ label: "alignment-free mapping mode where the position is reported without the CIGAR string",
+ }
+ ]
+ }
+ ],
+ 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
--
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