Skip to content

Commit

Permalink
Use gz files
Browse files Browse the repository at this point in the history
  • Loading branch information
endast committed Oct 16, 2023
1 parent 22b979a commit 5995e8b
Showing 1 changed file with 12 additions and 12 deletions.
24 changes: 12 additions & 12 deletions pipelines/annotations.snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ rule aggregate_and_merge_absplice:

rule merge_deepsea_pcas:
input:
annotations=anno_dir / "vep_deepripe.parquet",
annotations=anno_dir / "vep_deepripe.parquet",
deepsea_pcas=anno_dir / "deepSea_pca" / "deepsea_pca.parquet",
output:
anno_dir / "vep_deepripe_deepsea.parquet"
Expand All @@ -145,21 +145,21 @@ rule merge_deepsea_pcas:
"{input.deepsea_pcas}",
"{output}",
]
)
)

rule concat_annotations:
input:
pvcf = metadata_dir / config['pvcf_blocks_file'],
anno_dir = anno_dir,
vcf_files=
vcf_files=
expand([anno_dir / f"{vcf_pattern}_merged.parquet"],
zip,
chr=chromosomes,
block=block)
output: anno_dir / "vep_deepripe.parquet"
shell:
shell:
" ".join([
"python",
"python",
str(annotation_python_file),
"concat-annotations",
"{input.pvcf}",
Expand All @@ -172,10 +172,10 @@ rule concat_annotations:
rule merge_annotations:
input:
vep = anno_dir / (vcf_pattern + "_vep_anno.tsv"),
deepripe_parclip = anno_dir / (vcf_pattern + "_variants.parclip_deepripe.csv"),
deepripe_k5 = anno_dir / (vcf_pattern + "_variants.eclip_k5_deepripe.csv"),
deepripe_hg2 = anno_dir / (vcf_pattern + "_variants.eclip_hg2_deepripe.csv"),
variant_file = variant_file
deepripe_parclip = anno_dir / (vcf_pattern + "_variants.parclip_deepripe.csv.gz"),
deepripe_k5 = anno_dir / (vcf_pattern + "_variants.eclip_k5_deepripe.csv.gz"),
deepripe_hg2 = anno_dir / (vcf_pattern + "_variants.eclip_hg2_deepripe.csv.gz"),
variant_file = variant_file


output:
Expand Down Expand Up @@ -362,7 +362,7 @@ rule deepRiPe_parclip:
variants=anno_tmp_dir / (vcf_pattern + "_variants.vcf"),
fasta=fasta_dir / fasta_file_name,
output:
anno_dir / (vcf_pattern + "_variants.parclip_deepripe.csv"),
anno_dir / (vcf_pattern + "_variants.parclip_deepripe.csv.gz"),

shell:
f"mkdir -p {pybedtools_tmp_path/'parclip'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path/'parclip'} {saved_deepripe_models_path} {{threads}} 'parclip'"
Expand All @@ -373,7 +373,7 @@ rule deepRiPe_eclip_hg2:
variants=anno_tmp_dir / (vcf_pattern + "_variants.vcf"),
fasta=fasta_dir / fasta_file_name,
output:
anno_dir / (vcf_pattern + "_variants.eclip_hg2_deepripe.csv"),
anno_dir / (vcf_pattern + "_variants.eclip_hg2_deepripe.csv.gz"),
threads: lambda wildcards, attempt: n_jobs_deepripe * attempt
shell:
f"mkdir -p {pybedtools_tmp_path/'hg2'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir} {{input.fasta}} {pybedtools_tmp_path/'hg2'} {saved_deepripe_models_path} {{threads}} 'eclip_hg2'"
Expand All @@ -384,7 +384,7 @@ rule deepRiPe_eclip_k5:
variants=anno_tmp_dir / (vcf_pattern + "_variants.vcf"),
fasta=fasta_dir / fasta_file_name,
output:
anno_dir / (vcf_pattern + "_variants.eclip_k5_deepripe.csv"),
anno_dir / (vcf_pattern + "_variants.eclip_k5_deepripe.csv.gz"),

threads: lambda wildcards, attempt: n_jobs_deepripe * attempt
shell:
Expand Down

0 comments on commit 5995e8b

Please sign in to comment.