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PMBio · Sep 23, 2024 · 294566e · 294566e
1 parent 9a7d518
commit 294566e
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Showing 4 changed files with 33 additions and 20 deletions.
diff --git a/pipelines/annotations.snakefile b/pipelines/annotations.snakefile
@@ -204,7 +204,7 @@ if not gene_id_file:
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join(
                 [f"deeprvat_annotations", "create-gene-id-file", "{input}", "{output}"]
@@ -216,7 +216,7 @@ rule extract_with_header:
     output:
         anno_tmp_dir / "{file_stem}_variants_header.vcf.gz",
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         (
             load_bfc
@@ -231,7 +231,7 @@ rule extract_variants:
     output:
         anno_tmp_dir / "{file_stem}_variants.vcf",
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -248,7 +248,7 @@ rule strip_chr_name:
     output:
         anno_tmp_dir / "{file_stem}_stripped.vcf.gz",
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         load_hts + """ cut -c 4- {input} | awk -F'\\t' 'BEGIN {{OFS = FS}} {{$3 = "chr"$1"_"$2"_"$4"_"$5; print}}' |bgzip > {output} """
 
@@ -268,7 +268,7 @@ rule vep:
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -331,7 +331,7 @@ rule merge_annotations:
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         (
             "HEADER=$(grep  -n  '#Uploaded_variation' "
@@ -356,7 +356,7 @@ rule concat_annotations:
     resources:
         mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -384,7 +384,7 @@ if(include_deepSEA):
             annotations_in = anno_dir / "annotations.parquet",
             annotations_out = anno_dir / "annotations.parquet",
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join(
                 [
@@ -403,7 +403,7 @@ else:
         output: 
             chckpt = anno_dir / 'chckpts' / 'merge_deepsea_pcas.chckpt' 
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             'touch {output.chckpt}'
 
@@ -422,7 +422,7 @@ if (include_absplice):
         resources:
             mem_mb=lambda wildcards, attempt: 19_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join(
                 [
@@ -454,7 +454,7 @@ if af_mode is None:
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join(
                 [
@@ -483,7 +483,7 @@ if af_mode is None:
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
 
 
         shell:
@@ -508,7 +508,7 @@ if af_mode is None:
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join([f"deeprvat_annotations", "calculate-maf", "{params.annotations_in}", "{params.annotations_out}"])+ " && touch {output.chckpt}"
 
@@ -526,7 +526,7 @@ elif(af_mode == 'af_gnomade'):
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join([f"deeprvat_annotations", "calculate-maf","--af-column-name gnomADe_AF" , "{params.annotations_in}", "{params.annotations_out}"])+ " && touch {output.chckpt}"
 
@@ -544,7 +544,7 @@ elif(af_mode == 'af_gnomadg'):
         resources:
             mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
         conda:
-            "../deeprvat_annotations.yml"
+            "../docker/deeprvat_annotations.yml"
         shell:
             " ".join([f"deeprvat_annotations", "calculate-maf", "--af-column-name gnomADg_AF", "{params.annotations_in}", "{params.annotations_out}" ])+ " && touch {output.chckpt}"
 
@@ -563,7 +563,7 @@ rule add_gene_ids:
     resources:
         mem_mb=lambda wildcards, attempt: 19_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -589,7 +589,7 @@ rule filter_by_exon_distance:
     resources:
         mem_mb=lambda wildcards, attempt: 25_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -612,7 +612,7 @@ rule compute_plof_column:
         annotations_out = anno_dir / "annotations.parquet",
     resources: mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell: 'deeprvat_annotations compute-plof {params.annotations_in} {params.annotations_out} && touch {output.chckpt}'
 
 
@@ -630,7 +630,7 @@ rule select_rename_fill_columns:
     resources:
         mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
     conda:
-        "../deeprvat_annotations.yml"
+        "../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [

diff --git a/pipelines/annotations/absplice.snakefile b/pipelines/annotations/absplice.snakefile
@@ -16,6 +16,8 @@ rule aggregate_absplice_scores:
     threads: ncores_agg_absplice
     resources:
         mem_mb=lambda wildcards, attempt: 15_000 * (attempt + 1),
+    conda:
+        "../../docker/absplice_env.yml"
     shell:
         " ".join(
             [

diff --git a/pipelines/annotations/deepSEA.snakefile b/pipelines/annotations/deepSEA.snakefile
@@ -9,7 +9,8 @@ rule deepSea:
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
     conda:
-        "kipoi-veff2"
+        "../../docker/kipoi-veff2_env.yml"
+#        "kipoi-veff2"
     shell:
         "kipoi_veff2_predict {input.variants} {input.fasta} {output} -l 1000 -m 'DeepSEA/predict' -s 'diff'"
 
@@ -24,6 +25,8 @@ rule concat_deepSea:
         mem_mb=lambda wildcards, attempt: 50_000 * (attempt + 1),
     output:
         anno_dir / "all_variants.deepSea.parquet",
+    conda:
+        "../../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [
@@ -43,6 +46,8 @@ rule deepSea_PCA:
         deepSEA_tmp_dir / "deepsea_pca.parquet",
     resources:
         mem_mb=lambda wildcards, attempt: 50_000 * (attempt + 1),
+    conda:
+        "../../docker/deeprvat_annotations.yml"
     shell:
         " ".join(
             [

diff --git a/pipelines/annotations/deepripe.snakefile b/pipelines/annotations/deepripe.snakefile
@@ -7,6 +7,8 @@ rule deepRiPe_parclip:
     threads: n_jobs_deepripe
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
+    conda:
+        "../../docker/deeprvat_annotations.yml"
     shell:
         f"mkdir -p {pybedtools_tmp_path/ 'parclip'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir}  {{input.fasta}} {pybedtools_tmp_path/ 'parclip'} {saved_deepripe_models_path} {{threads}} 'parclip'"
 
@@ -20,6 +22,8 @@ rule deepRiPe_eclip_hg2:
     threads: lambda wildcards, attempt: n_jobs_deepripe * attempt
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
+    conda:
+        "../../docker/deeprvat_annotations.yml"
     shell:
         f"mkdir -p {pybedtools_tmp_path/ 'hg2'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir}  {{input.fasta}} {pybedtools_tmp_path/ 'hg2'} {saved_deepripe_models_path} {{threads}} 'eclip_hg2'"
 
@@ -33,6 +37,8 @@ rule deepRiPe_eclip_k5:
     threads: lambda wildcards, attempt: n_jobs_deepripe * attempt
     resources:
         mem_mb=lambda wildcards, attempt: 5_000 * (attempt + 1),
+    conda:
+        "../../docker/deeprvat_annotations.yml"
     shell:
         f"mkdir -p {pybedtools_tmp_path/ 'k5'} && deeprvat_annotations scorevariants-deepripe {{input.variants}} {anno_dir}  {{input.fasta}} {pybedtools_tmp_path/ 'k5'} {saved_deepripe_models_path} {{threads}} 'eclip_k5'"