remove LSF-specific memory directives from params

rnabioco · Nov 14, 2023 · 252bcc1 · 252bcc1
1 parent 7bca704
commit 252bcc1
Show file tree

Hide file tree

Showing 4 changed files with 48 additions and 35 deletions.
diff --git a/rules/check_versions.snake b/rules/check_versions.snake
@@ -7,9 +7,10 @@ rule check:
      checked = "{data}/check_versions.txt"
    params:
      job_name = "check",
-     memory = "select[mem>5] rusage[mem=5]", # LSF format; change as needed
    log:
      "{data}/logs/check_versions.txt"
+   resources:
+     mem_mb = 5000
    threads:
      1
    shell:

diff --git a/rules/count.snake b/rules/count.snake
@@ -13,13 +13,14 @@ rule assign_sites_R1:
     bam = temp("{results}/temp/{sample}_R1_assigned.bam")
   params:
     job_name = "assign_sites_R1",
-    memory = "select[mem>8] rusage[mem=8]", # LSF format; change as needed
     out = "{results}/temp/{sample}_R1_assigned",
     out_bam = "{results}/temp/{sample}_R1.bam.featureCounts.bam"
   log:
     "{results}/logs/assign_sites_{sample}_R1.txt"
   threads:
     12
+  resources:
+    mem_mb = 8000
   shell:
     """
     if echo {POLYA_SITES} | tr '[:upper:]' '[:lower:]' | grep -q -e "\.saf$" -e "\.saf.gz$"; then
@@ -53,13 +54,14 @@ rule assign_sites_R2:
     bam = temp("{results}/temp/{sample}_R2_assigned.bam")
   params:
     job_name = "assign_sites_R2",
-    memory = "select[mem>8] rusage[mem=8]", # LSF format; change as needed
     out = "{results}/temp/{sample}_R2_assigned",
     out_bam = "{results}/temp/{sample}_R2.bam.featureCounts.bam"
   log:
     "{results}/logs/assign_sites_{sample}_R2.txt"
   threads:
     12
+  resources:
+    mem_mb = 8000
   shell:
     """
     if echo {POLYA_SITES} | tr '[:upper:]' '[:lower:]' | grep -q -e "\.saf$" -e "\.saf.gz$"; then
@@ -94,13 +96,14 @@ rule assign_sites_paired:
     bam = temp("{results}/temp/{sample}_paired_assigned.bam")
   params:
     job_name = "assign_sites_paired",
-    memory = "select[mem>8] rusage[mem=8]", # LSF format; change as needed
     out = "{results}/temp/{sample}_paired_assigned",
     out_bam = "{results}/temp/{sample}_paired.bam.featureCounts.bam"
   log:
     "{results}/logs/assign_sites_{sample}_paired.txt"
   threads:
     12
+  resources:
+    mem_mb = 8000
   shell:
     """
     if echo {POLYA_SITES} | tr '[:upper:]' '[:lower:]' | grep -q -e "\.saf$" -e "\.saf.gz$"; then
@@ -137,12 +140,13 @@ rule filter_R1:
     length = _get_chem_length_R1,
     temp = "{results}/temp/{sample}_R1_filter.bam",
     temp2 = "{results}/temp/{sample}_R1_filter2.bam",
-    final = "{results}/counts/{sample}_R1_counts.tsv.gz",
-    memory = "select[mem>8] rusage[mem=8]" # LSF format; change as needed
+    final = "{results}/counts/{sample}_R1_counts.tsv.gz"
   log:
     "{results}/logs/filter_{sample}_R1.txt"
   threads:
     4
+  resources:
+    mem_mb = 8000
   shell:
     """
     samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
@@ -168,12 +172,13 @@ rule filter_R2:
   params:
     job_name = "filter",
     temp = "{results}/temp/{sample}_R2_filter.bam",
-    tempbai = "{results}/temp/{sample}_R2_filter.bam.bai",
-    memory = "select[mem>8] rusage[mem=8]" # LSF format; change as needed
+    tempbai = "{results}/temp/{sample}_R2_filter.bam.bai"
   log:
     "{results}/logs/filter_{sample}_R2.txt"
   threads:
     4
+  resources:
+    mem_mb = 8000
   shell:
     """
     samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
@@ -194,12 +199,13 @@ rule filter_paired:
     length = _get_chem_length_R1,
     temp = "{results}/temp/{sample}_paired_filter.bam",
     temp2 = "{results}/temp/{sample}_paired_filter2.bam",
-    final = "{results}/counts/{sample}_paired_counts.tsv.gz",
-    memory = "select[mem>8] rusage[mem=8]" # LSF format; change as needed
+    final = "{results}/counts/{sample}_paired_counts.tsv.gz"
   log:
     "{results}/logs/filter_{sample}_paired.txt"
   threads:
     4
+  resources:
+    mem_mb = 8000
   shell:
     """
     samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
@@ -223,12 +229,13 @@ rule count:
   output:
     "{results}/counts/{sample}_{read}_counts.tsv.gz"
   params:
-    job_name = "count",
-    memory = "select[mem>8] rusage[mem=8]" # LSF format; change as needed
+    job_name = "count"
   log:
     "{results}/logs/count_{sample}_{read}.txt"
   threads:
     4
+  resources:
+    mem_mb = 8000
   shell:
     """
     umi_tools count \
@@ -252,12 +259,13 @@ rule bed_R1:
   params:
     job_name = "bed",
     dedup = "{results}/temp/{sample}_R1_dedup.bam",
-    r = "{results}/temp/{sample}_R1_r.bam",
-    memory = "select[mem>48] rusage[mem=48]" # LSF format; change as needed
+    r = "{results}/temp/{sample}_R1_r.bam"
   log:
     "{results}/logs/bed_{sample}_R1.txt"
   threads:
     4
+  resources:
+    mem_mb = 48000
   shell:
     """
     umi_tools dedup \
@@ -283,12 +291,13 @@ rule bed_R2:
     "{results}/bed/{sample}_R2.bed.gz"
   params:
     job_name = "bed",
-    dedup = "{results}/temp/{sample}_R2_dedup.bam",
-    memory = "select[mem>48] rusage[mem=48]" # LSF format; change as needed
+    dedup = "{results}/temp/{sample}_R2_dedup.bam"
   log:
     "{results}/logs/bed_{sample}_R2.txt"
   threads:
     4
+  resources:
+    mem_mb = 48000
   shell:
     """
     umi_tools dedup \
@@ -312,12 +321,13 @@ rule bed_paired:
   params:
     job_name = "bed",
     dedup = "{results}/temp/{sample}_paired_dedup.bam",
-    r = "{results}/temp/{sample}_paired_r.bam",
-    memory = "select[mem>48] rusage[mem=48]" # LSF format; change as needed
+    r = "{results}/temp/{sample}_paired_r.bam"
   log:
     "{results}/logs/bed_{sample}_paired.txt"
   threads:
     4
+  resources:
+    mem_mb = 48000
   shell:
     """
     umi_tools dedup \
@@ -334,4 +344,4 @@ rule bed_paired:
     samtools view -f 0x42 {params.dedup} -b > {params.r}
     bedtools genomecov -ibam {params.r} -5 -dz | awk 'BEGIN {{ OFS = "\t" }} {{ print $1, $2 - 1, $2, $3 }}' - | gzip > {output}
     rm -rf {params.r}
-    """
+    """
diff --git a/rules/cutadapt_star.snake b/rules/cutadapt_star.snake
@@ -50,18 +50,19 @@ rule cutadapt_R1:
       job_name = "cutadapt",
       bc_cut = _get_bc_cut,
       info = "{results}/cutadapt/temp_{sample}_R1.info",
-      temp = "{results}/cutadapt/temp_{sample}_R1_trimmed.R1.fastq.gz",
-      memory = "select[mem>32] rusage[mem=32]"
+      temp = "{results}/cutadapt/temp_{sample}_R1_trimmed.R1.fastq.gz"
     log: "{results}/logs/{sample}_cutadapt.out"
     threads: 24
+    resources:
+      mem_mb = 32000
     shell:
       """
       cutadapt -j 24 \
         -a TSO_R1=CCCATGTACTCTGCGTTGATACCACTGCTT \
         -a TruSeq_R1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
         -n 4 \
         -m 75 \
-	-l 300 \
+	    -l 300 \
         --nextseq-trim=20 \
         -o {output.R1} \
         <(zcat {input})
@@ -79,10 +80,11 @@ rule cutadapt_paired:
       bc_cut = _get_bc_cut,
       info = "{results}/cutadapt/temp_{sample}_paired.info",
       temp = "{results}/cutadapt/temp_{sample}_paired_trimmed.R1.fastq.gz",
-      temp2 = "{results}/cutadapt/temp_{sample}_paired_trimmed.R2.fastq.gz",
-      memory = "select[mem>32] rusage[mem=32]"
+      temp2 = "{results}/cutadapt/temp_{sample}_paired_trimmed.R2.fastq.gz"
     log: "{results}/logs/{sample}_cutadapt.out"
     threads: 24
+    resources:
+      mem_mb = 32000
     shell:
       """
       if [ -z "{params.bc_cut}" ] ; then
@@ -131,11 +133,11 @@ rule starsolo_R1:
       chemistry = _get_chem_version_R1,
       extra_args = _get_extra_args,
       out_dir = "{results}/{sample}/{sample}_R1_",
-      job_name = "star_R1",
-      memory = "select[mem>48] rusage[mem=48]"
+      job_name = "star_R1"
     log: "{results}/logs/{sample}_star_R1.out"
     resources:
-      total_impact = 5
+      total_impact = 5,
+      mem_mb = 48000
     threads: 14
     shell:
       """
@@ -174,11 +176,11 @@ rule starsolo_R2:
       chemistry = _get_chem_version_R2,
       extra_args = _get_extra_args,
       out_dir = "{results}/{sample}/{sample}_R2_", 
-      job_name = "star_R2",
-      memory = "select[mem>48] rusage[mem=48]"
+      job_name = "star_R2"
     log: "{results}/logs/{sample}_star_R2.out"
     resources:
-      total_impact = 5
+      total_impact = 5,
+      mem_mb = 48000
     threads: 14
     shell:
       """
@@ -215,12 +217,11 @@ rule starsolo_paired:
       chemistry = _get_chem_version_R1,
       extra_args = _get_extra_args,
       out_dir = "{results}/{sample}/{sample}_paired_", 
-      job_name = "star_paired",
-      memory = 
-      "select[mem>48] rusage[mem=48]"
+      job_name = "star_paired"
     log: "{results}/logs/{sample}_star_paired.out"
     resources:
-      total_impact = 5
+      total_impact = 5,
+      mem_mb = 48000
     threads: 14
     shell:
       """

diff --git a/rules/qc.snake b/rules/qc.snake
@@ -9,11 +9,12 @@ rule qc_check:
      job_name = "qc",
      target = "{results}",
      path = "{results}/report",
-     memory = "select[mem>5] rusage[mem=5]", # LSF format; change as needed
    log:
      "{results}/logs/multiqc.txt"
    threads:
      1
+   resources:
+     mem_mb = 5000
    shell:
      """
      export LC_ALL=en_US.utf-8