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fiberseq · Dec 3, 2024 · 74c3b4f · 74c3b4f
1 parent 6087cba
commit 74c3b4f
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/workflow/rules/apply-model.smk b/workflow/rules/apply-model.smk
@@ -6,7 +6,7 @@ rule fire:
         bam=ancient(get_input_bam),
     output:
         bam=temp("temp/{sm}/fire/{chrom}.fire.bam"),
-    threads: 6
+    threads: 4
     resources:
         mem_mb=8 * 1024,
     params:
@@ -92,7 +92,7 @@ rule fire_sites:
         ),
     output:
         bed="results/{sm}/additional-outputs-{v}/fire-peaks/{sm}-{v}-fire-elements.bed.gz",
-    threads: 8
+    threads: 1
     conda:
         DEFAULT_ENV
     shell:

diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk
@@ -141,7 +141,7 @@ rule pileup:
         fofn=temp("temp/{sm}/fire/fire-{v}-pileup.fofn"),
         bed="results/{sm}/{sm}-fire-{v}-pileup.bed.gz",
         tbi="results/{sm}/{sm}-fire-{v}-pileup.bed.gz.tbi",
-    threads: 8
+    threads: 4
     conda:
         DEFAULT_ENV
     shell:
@@ -252,7 +252,7 @@ rule fire_peaks:
         fofn=temp("temp/{sm}/fire-peaks/{sm}-fire-{v}-peaks.fofn"),
         bed="results/{sm}/{sm}-fire-{v}-peaks.bed.gz",
         tbi="results/{sm}/{sm}-fire-{v}-peaks.bed.gz.tbi",
-    threads: 8
+    threads: 4
     conda:
         DEFAULT_ENV
     shell:
@@ -356,7 +356,7 @@ rule peaks_vs_percent:
             "results/{sm}/additional-outputs-{v}/figures/{sm}-fire-{v}-peaks-vs-percent.pdf",
             category="Peak calls",
         ),
-    threads: 8
+    threads: 4
     conda:
         "../envs/R.yaml"
     script:

diff --git a/workflow/rules/stats.smk b/workflow/rules/stats.smk
@@ -9,7 +9,7 @@ rule clustering_vs_null:
         tmp=temp("temp/{sm}/tmp.pre.calls.bed"),
         null=temp("temp/{sm}/null.calls.bed"),
         bed="results/{sm}/clustering-vs-null.bed.gz",
-    threads: 8
+    threads: 4
     conda:
         DEFAULT_ENV
     shell:
@@ -33,7 +33,7 @@ rule fires_in_peaks:
     output:
         tmp=temp("temp/{sm}/tmp.FIREs-{v}-in-peaks.bed"),
         txt="results/{sm}/additional-outputs-{v}/fire-peaks/{sm}-{v}-fires-in-peaks.txt",
-    threads: 8
+    threads: 4
     conda:
         DEFAULT_ENV
     params:
@@ -78,7 +78,7 @@ rule hap_differences:
         ),
         bed="results/{sm}/{sm}-fire-{v}-hap-differences.bed.gz",
         bed9=temp("temp/{sm}/hap1-vs-hap2/FIRE-{v}.hap.differences.bed9"),
-    threads: 8
+    threads: 4
     conda:
         "../envs/R.yaml"
     script: