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22 allow for fa and fasta extensions in host dir #23

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merged 5 commits into from
Jun 5, 2024
Merged

22 allow for fa and fasta extensions in host dir #23

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5130ada
Run tests on push to main
Ulthran Jun 5, 2024
83de856
Trigger pr workflow on all proper events
Ulthran Jun 5, 2024
e588c26
Include .fa and .fasta genomes
Ulthran Jun 5, 2024
684336d
Allow .fasta OR .fa (not both)
Ulthran Jun 5, 2024
179092b
Track new host file ext
Ulthran Jun 5, 2024
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6 changes: 2 additions & 4 deletions .github/workflows/pr.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,9 @@ name: Tests

on:
pull_request:
branches:
- main
branches: [ master, main ]
push:
branches:
- main
branches: [ master, main ]

jobs:
run-tests:
Expand Down
49 changes: 25 additions & 24 deletions sbx_mapping.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -15,26 +15,26 @@ def get_mapping_path() -> Path:


SBX_MAPPING_VERSION = open(get_mapping_path() / "VERSION").read().strip()

try:
GenomeFiles
GenomeSegments
except NameError:
sys.stderr.write("sbx_mapping::INFO Collecting target genomes... ")
if (
Cfg["sbx_mapping"]["genomes_fp"] == Cfg["all"]["root"]
or not Cfg["sbx_mapping"]["genomes_fp"]
):
GenomeFiles = []
GenomeSegments = {}
else:
GenomeFiles = [f for f in Cfg["sbx_mapping"]["genomes_fp"].glob("*.fasta")]
GenomeSegments = {
PurePath(g.name).stem: read_seq_ids(Cfg["sbx_mapping"]["genomes_fp"] / g)
for g in GenomeFiles
}
sys.stderr.write("done.\n")
sys.stderr.write(f"sbx_mapping::INFO Genome files found: {str(GenomeFiles)}\n")
HOST_FILE_EXT = ".fasta"
sys.stderr.write("sbx_mapping::INFO Collecting target genomes... ")
if (
Cfg["sbx_mapping"]["genomes_fp"] == Cfg["all"]["root"]
or not Cfg["sbx_mapping"]["genomes_fp"]
):
GenomeFiles = []
GenomeSegments = {}
else:
GenomeFiles = [f for f in Cfg["sbx_mapping"]["genomes_fp"].glob("*.fasta")]
if not GenomeFiles:
GenomeFiles = [f for f in Cfg["sbx_mapping"]["genomes_fp"].glob("*.fa")]
HOST_FILE_EXT = ".fa"
GenomeSegments = {
PurePath(g.name).stem: read_seq_ids(Cfg["sbx_mapping"]["genomes_fp"] / g)
for g in GenomeFiles
}
GenomeFiles = {PurePath(g.name).stem: g for g in GenomeFiles}
sys.stderr.write("done.\n")
sys.stderr.write(f"sbx_mapping::INFO Genome files found: {str(GenomeFiles)}\n")


try:
Expand Down Expand Up @@ -80,10 +80,10 @@ rule all_mapping:

rule build_genome_index:
input:
Cfg["sbx_mapping"]["genomes_fp"] / "{genome}.fasta",
Cfg["sbx_mapping"]["genomes_fp"] / ("{genome}" + HOST_FILE_EXT),
output:
[
Cfg["sbx_mapping"]["genomes_fp"] / ("{genome}.fasta." + ext)
Cfg["sbx_mapping"]["genomes_fp"] / ("{genome}" + HOST_FILE_EXT + "." + ext)
for ext in ["amb", "ann", "bwt", "pac", "sa"]
],
benchmark:
Expand All @@ -100,8 +100,8 @@ rule build_genome_index:

rule align_to_genome:
input:
*rules.build_genome_index.output,
reads=expand(QC_FP / "decontam" / "{{sample}}_{rp}.fastq.gz", rp=Pairs),
index=Cfg["sbx_mapping"]["genomes_fp"] / "{genome}.fasta.amb",
output:
temp(MAPPING_FP / "intermediates" / "{genome}" / "{sample}.sam"),
benchmark:
Expand All @@ -110,6 +110,7 @@ rule align_to_genome:
LOG_FP / "align_to_genome_{genome}_{sample}.log",
params:
index_fp=Cfg["sbx_mapping"]["genomes_fp"],
host_file_ext=HOST_FILE_EXT,
threads: 4
conda:
"envs/sbx_mapping_env.yml"
Expand All @@ -118,7 +119,7 @@ rule align_to_genome:
shell:
"""
bwa mem -M -t {threads} \
{params.index_fp}/{wildcards.genome}.fasta \
{params.index_fp}/{wildcards.genome}{params.host_file_ext} \
{input.reads} -o {output} \
2>&1 | tee {log}
"""
Expand Down
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