Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Metagenomics
snakemake
Commits
60b2f40e
Commit
60b2f40e
authored
Aug 09, 2021
by
Kenzo-Hugo Hillion
♻
Browse files
fix bamtofastq_pairs
parent
93e24e41
Changes
2
Hide whitespace changes
Inline
Side-by-side
tools/bedtools/bamtofastq_pairs/Snakefile
View file @
60b2f40e
...
...
@@ -7,9 +7,11 @@ rule bedtools_bamtofastq_pairs:
input:
__bedtools_bamtofastq_pairs_input
output:
forward = __bedtools_bamtofastq_pairs_output_forward,
reverse = __bedtools_bamtofastq_pairs_output_reverse
forward =
f"{
__bedtools_bamtofastq_pairs_output_forward
_name}.fq.gz"
,
reverse =
f"{
__bedtools_bamtofastq_pairs_output_reverse
_name}.fq.gz"
params:
forward_name = __bedtools_bamtofastq_pairs_output_forward_name,
reverse_name = __bedtools_bamtofastq_pairs_output_reverse_name,
exec_command = __bedtools_bamtofastq_pairs_bedtools_exec_command,
modules = __bedtools_bamtofastq_pairs_modules
run:
...
...
@@ -17,8 +19,8 @@ rule bedtools_bamtofastq_pairs:
if params.modules:
command.append("module load {params.modules}")
command.append(
"{params.exec_command} bamtofastq -i {input} -fq {
output
.forward}.f
ast
q -fq2 {
output
.reverse}.f
ast
q"
"{params.exec_command} bamtofastq -i {input} -fq {
params
.forward
_name
}.fq -fq2 {
params
.reverse
_name
}.fq"
)
command.append("g
un
zip {
output}_1.fast
q")
command.append("g
un
zip {
output}_2.fast
q")
command.append("gzip {
params.forward_name}.f
q")
command.append("gzip {
params.reverse_name}.f
q")
shell(" && ".join(command))
\ No newline at end of file
tools/bedtools/bamtofastq_pairs/example_usage/Snakefile
View file @
60b2f40e
...
...
@@ -12,8 +12,15 @@ __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}")
__bedtools_bamtofastq_pairs_output_forward_name = "{dir}/{{sample}}_1".format(
dir=__bedtools_bamtofastq_pairs_output_dir, sample="{sample}"
)
__bedtools_bamtofastq_pairs_output_reverse_name = "{dir}/{{sample}}_2".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)
input:
forward = expand(f"{__bedtools_bamtofastq_pairs_output_forward_name}.fq.gz", sample=SAMPLES),
reverse = expand(f"{__bedtools_bamtofastq_pairs_output_reverse_name}.fq.gz", sample=SAMPLES)
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment