From 93e24e418eafba95827078676363575e67e62dbe Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Mon, 2 Aug 2021 12:12:19 +0200
Subject: [PATCH] start bedtools bamtofastq
---
tools/bedtools/bamtofastq_pairs/Snakefile | 24 +++++++++++++++++++
.../bamtofastq_pairs/example_usage/Snakefile | 19 +++++++++++++++
.../example_usage/config.yaml | 14 +++++++++++
.../example_usage/Snakefile | 2 +-
4 files changed, 58 insertions(+), 1 deletion(-)
create mode 100644 tools/bedtools/bamtofastq_pairs/Snakefile
create mode 100644 tools/bedtools/bamtofastq_pairs/example_usage/Snakefile
create mode 100644 tools/bedtools/bamtofastq_pairs/example_usage/config.yaml
diff --git a/tools/bedtools/bamtofastq_pairs/Snakefile b/tools/bedtools/bamtofastq_pairs/Snakefile
new file mode 100644
index 0000000..55878f8
--- /dev/null
+++ b/tools/bedtools/bamtofastq_pairs/Snakefile
@@ -0,0 +1,24 @@
+__bedtools_bamtofastq_pairs_bedtools_exec_command = config.get(
+ 'bedtools_bamtofastq_pairs', {}
+).get('bedtools_exec_command', 'bedtools')
+__bedtools_bamtofastq_pairs_modules = config.get('bedtools_bamtofastq_pairs', {}).get('modules')
+
+rule bedtools_bamtofastq_pairs:
+ input:
+ __bedtools_bamtofastq_pairs_input
+ output:
+ forward = __bedtools_bamtofastq_pairs_output_forward,
+ reverse = __bedtools_bamtofastq_pairs_output_reverse
+ params:
+ exec_command = __bedtools_bamtofastq_pairs_bedtools_exec_command,
+ modules = __bedtools_bamtofastq_pairs_modules
+ run:
+ command = []
+ if params.modules:
+ command.append("module load {params.modules}")
+ command.append(
+ "{params.exec_command} bamtofastq -i {input} -fq {output.forward}.fastq -fq2 {output.reverse}.fastq"
+ )
+ command.append("gunzip {output}_1.fastq")
+ command.append("gunzip {output}_2.fastq")
+ shell(" && ".join(command))
\ No newline at end of file
diff --git a/tools/bedtools/bamtofastq_pairs/example_usage/Snakefile b/tools/bedtools/bamtofastq_pairs/example_usage/Snakefile
new file mode 100644
index 0000000..11262fc
--- /dev/null
+++ b/tools/bedtools/bamtofastq_pairs/example_usage/Snakefile
@@ -0,0 +1,19 @@
+configfile: "config.yaml"
+
+# ==== Snakefile path ====
+__bedtools_bamtofastq_pairs_rules = config.get("snakefiles", {}).get("bedtools_bamtofastq_pairs")
+
+__main_output_dir = config.get('output_dir', 'output')
+
+# ==== Main config ====
+SAMPLES = config.get('samples')
+__input_dir = config.get('input_dir', 'data')
+
+# ==== Bedtools bamtofastq ====
+__bedtools_bamtofastq_pairs_output_dir = f"{__main_output_dir}/bedtools_bamtofastq_pairs"
+__bedtools_bamtofastq_pairs_input = "{dir}/{{sample}}.bam".format(dir=__input_dir, sample="{sample}")
+__bedtools_bamtofastq_pairs_output = "{dir}/{{sample}}".format(dir=__bedtools_bamtofastq_pairs_output_dir, sample="{sample}")
+include: __bedtools_bamtofastq_pairs_rules
+
+rule all:
+ input: expand("{dir}/{{sample}}_unmapped.bam".format(dir=__bedtools_bamtofastq_pairs_output_dir), sample=SAMPLES)
diff --git a/tools/bedtools/bamtofastq_pairs/example_usage/config.yaml b/tools/bedtools/bamtofastq_pairs/example_usage/config.yaml
new file mode 100644
index 0000000..b576b74
--- /dev/null
+++ b/tools/bedtools/bamtofastq_pairs/example_usage/config.yaml
@@ -0,0 +1,14 @@
+snakefiles:
+ bedtools_bamtofastq_pairs: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/bedtools/bamtofastq_pairs/Snakefile
+
+input_dir: /some/input/directory
+output_dir: /some/output/directory
+
+samples:
+- test_00000
+- test_00001
+- test_00002
+
+bedtools_bamtofastq_pairs:
+ bedtools_exec_command: bedtools
+ modules: bedtools
diff --git a/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile b/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
index dabd02c..d998d29 100644
--- a/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
+++ b/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
@@ -16,4 +16,4 @@ __extract_unmapped_pairs_output = "{dir}/{{sample}}_unmapped.bam".format(dir=__e
include: __extract_unmapped_pairs_rules
rule all:
- input: expand("{dir}/{{sample}}_unmapped.bam".format(dir=__input_dir), sample=SAMPLES)
+ input: expand("{dir}/{{sample}}_unmapped.bam".format(dir=__extract_unmapped_pairs_output_dir), sample=SAMPLES)
--
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