From 41296111143f333d6b549ec0bfc58a7198ef5e20 Mon Sep 17 00:00:00 2001
From: Brian Fulton-Howard <fultonh1@gmail.com>
Date: Thu, 15 May 2025 11:10:03 -0400
Subject: [PATCH 1/6] Update for compatibility with Snakemake 8+

---
 workflow/Snakefile      | 52 ++++++++++++++++++++---------------------
 workflow/rules/bgen.smk | 10 ++++----
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index b4fef4b..8942b89 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -172,7 +172,7 @@ if zipped:
         conda: 'envs/p7z.yaml'
         threads: 4
         resources:
-            mem_mb = 4000,
+            mem_mb = 16000,
             time_min = 5
         shell:
             r'''
@@ -217,8 +217,8 @@ rule stats:
     conda: "envs/r_stats.yaml"
     threads: 22
     resources:
-        mem_mb = 8000,
-        walltime = '8:00'
+        mem_mb = 176000,
+        runtime: "8h"
     script: "scripts/Post_imputation.Rmd"
 
 # Sample filtering rules
@@ -244,7 +244,7 @@ rule fixheaders:
     threads: 1
     resources:
         mem_mb = 2048,
-        walltime = '24:00'
+        runtime: "24h"
     conda: "envs/bcftools.yaml"
     shell:
         r"""
@@ -270,7 +270,7 @@ if minimac_version == 'guess':
         threads: 1
         resources:
             mem_mb = 2048,
-            walltime = '24:00'
+            runtime: "24h"
         script: 'scripts/rule_detect_minimac.py'
 else:
     rule detect_minimac:
@@ -282,7 +282,7 @@ else:
         localrule: True
         resources:
             mem_mb = 2048,
-            walltime = '1:00'
+            runtime: "1h"
         shell: 'echo {params.ver} > {output}'
 
 
@@ -299,8 +299,8 @@ if sampfilt and minimac_version in ['guess', '3']:
             sf = sampfilt
         threads: 8
         resources:
-            mem_mb = 256,
-            walltime = '24:00'
+            mem_mb = 2048,
+            runtime: "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -332,8 +332,8 @@ elif minimac_version in ['guess', '3']:
             filt = qualfilt
         threads: 8
         resources:
-            mem_mb = 256,
-            walltime = '24:00'
+            mem_mb = 2048,
+            runtime: "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -364,8 +364,8 @@ elif sampfilt:
             sf = sampfilt
         threads: 8
         resources:
-            mem_mb = 256,
-            walltime = '24:00'
+            mem_mb = 2048,
+            runtime: "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -385,8 +385,8 @@ else:
             filt = qualfilt
         threads: 8
         resources:
-            mem_mb = 256,
-            walltime = '24:00'
+            mem_mb = 2048,
+            runtime: "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -429,7 +429,7 @@ rule rename:
     conda: "envs/bcftools.yaml"
     threads: 2
     resources:
-        mem_mb = 1024,
+        mem_mb = 2048,
         time_min = 60
     shell:
         '''
@@ -460,7 +460,7 @@ rule renameAuto:
     conda: "envs/bcftools.yaml"
     threads: 2
     resources:
-        mem_mb = 1024,
+        mem_mb = 2048,
         time_min = 60
     shell:
         '''
@@ -473,8 +473,8 @@ rule concat_chroms_samp:
     output: "{impute_dir}/data/{cohort}_chrall_filtered.vcf.gz"
     threads: 8
     resources:
-        mem_mb = 512,
-        walltime = '24:00'
+        mem_mb = 4096,
+        runtime: "24h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools concat --threads 8 {input} | bcftools norm -d none -o {output} -Oz"
 
@@ -495,8 +495,8 @@ rule merge_samples_chrom:
     output: "{impute_dir}/data/by_chrom/all_chr{chrom}_filtered.vcf.gz"
     threads: 8
     resources:
-        mem_mb = 2000,
-        walltime = "36:00"
+        mem_mb = 16000,
+        runtime: "36h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools merge -m none --threads 8 {input.vcf} | bcftools norm -d none -o {output} -Oz"
 
@@ -505,8 +505,8 @@ rule concat_chroms_all:
     output: "{impute_dir}/data/all_chrall_filtered.vcf.gz"
     threads: 8
     resources:
-        mem_mb = 256,
-        walltime = "24:00"
+        mem_mb = 2048,
+        runtime: "24h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools concat -o {output} -Oz --threads 8 {input}"
 
@@ -518,8 +518,8 @@ rule make_plink_all:
         ID = "--id-delim" if automap_tf else "--double-id"
     threads: 10
     resources:
-        mem_mb = 3000,
-        walltime = "96:00"
+        mem_mb = 30000,
+        runtime: "96h"
     conda: "envs/plink.yaml"
     shell:
         "plink --keep-allele-order --vcf {input} {params.ID} --memory 20000 --threads 10 --make-bed "
@@ -533,8 +533,8 @@ rule make_plink_samp:
         ID = "--id-delim" if automap_tf else "--double-id "
     threads: 10
     resources:
-        mem_mb = 2000,
-        walltime = "2:00"
+        mem_mb = 20000,
+        runtime: "2h"
     conda: "envs/plink.yaml"
     shell:
         "plink --keep-allele-order --vcf {input} {params.ID} --memory 20000 --threads 10 --make-bed "
diff --git a/workflow/rules/bgen.smk b/workflow/rules/bgen.smk
index b32551c..5b2d80f 100644
--- a/workflow/rules/bgen.smk
+++ b/workflow/rules/bgen.smk
@@ -8,7 +8,7 @@ rule make_bgen:
     threads: 1
     resources:
         mem_mb = 4000,
-        walltime = "24:00"
+        runtime: "24h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -26,7 +26,7 @@ rule cat_bgen_samp:
     threads: 1
     resources:
         mem_mb = 5000,
-        walltime = "120:00"
+        runtime: "120h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -47,8 +47,8 @@ rule make_bgen_allsamp:
         args = " ".join(["-g {} -s {}".format(gen, samp) for gen, samp in zip(bga_gen, bga_samp)])
     threads: 10
     resources:
-        mem_mb = 4000,
-        walltime = "24:00"
+        mem_mb = 40000,
+        runtime: "24h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -65,6 +65,6 @@ rule cat_bgen_allsamp:
     threads: 1
     resources:
         mem_mb = 5000,
-        walltime = "120:00"
+        runtime: "120h"
     container: 'docker://befh/bgen:v1.1.7'
     shell: "cat-bgen -g {input.gen} -og {output.gen}; cp {input.samp} {output.samp}"

From 362277452104ae4e03f035a483a4b8d89c6aba9e Mon Sep 17 00:00:00 2001
From: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Date: Tue, 3 Jun 2025 13:58:49 -0400
Subject: [PATCH 2/6] fixed issue with runtime resource and added ability to
 directly fix fams

---
 workflow/Snakefile      | 65 +++++++++++++++++++++++++++++++----------
 workflow/rules/bgen.smk |  8 ++---
 2 files changed, 54 insertions(+), 19 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 8942b89..d1ae365 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -136,14 +136,23 @@ if config["qc"]["rsq2"] and config["qc"]["rsq2"] != 'NA':
     qualfilt += " || (R2 >= {R2} && MAF < {MAF})".format(
         R2=config["qc"]["rsq2"], MAF=config["qc"]["maf"])
 
+
+if "fix_fam" in config and config["fix_fam"]:
+    path_plink_bycohort = "{impute_dir}/data/{cohort}_chrall_filtered_fixed.{ext}"
+    path_plink_merged = "{impute_dir}/data/all_chrall_filtered_fixed.{ext}"
+else:
+    path_plink_bycohort = "{impute_dir}/data/{cohort}_chrall_filtered.{ext}"
+    path_plink_merged = "{impute_dir}/data/all_chrall_filtered.{ext}"
+
+
 outs = dict(
     stat_report="{impute_dir}/stats/{cohort}_impStats.html",
     vcf_bycohort="{impute_dir}/data/{cohort}_chrall_filtered.vcf.gz",
     vcf_merged="{impute_dir}/data/all_chrall_filtered.vcf.gz",
     bgen_bycohort="{impute_dir}/data/{cohort}_chrall_filtered.bgen",
     bgen_merged="{impute_dir}/data/merged/merged_chrall_filtered.bgen",
-    plink_bycohort="{impute_dir}/data/{cohort}_chrall_filtered.{ext}",
-    plink_merged="{impute_dir}/data/all_chrall_filtered.{ext}")
+    plink_bycohort=path_plink_bycohort,
+    plink_merged=path_plink_merged)
 
 
 def expand_outs(out):
@@ -218,7 +227,7 @@ rule stats:
     threads: 22
     resources:
         mem_mb = 176000,
-        runtime: "8h"
+        runtime = "8h"
     script: "scripts/Post_imputation.Rmd"
 
 # Sample filtering rules
@@ -244,7 +253,7 @@ rule fixheaders:
     threads: 1
     resources:
         mem_mb = 2048,
-        runtime: "24h"
+        runtime = "24h"
     conda: "envs/bcftools.yaml"
     shell:
         r"""
@@ -270,7 +279,7 @@ if minimac_version == 'guess':
         threads: 1
         resources:
             mem_mb = 2048,
-            runtime: "24h"
+            runtime = "24h"
         script: 'scripts/rule_detect_minimac.py'
 else:
     rule detect_minimac:
@@ -282,7 +291,7 @@ else:
         localrule: True
         resources:
             mem_mb = 2048,
-            runtime: "1h"
+            runtime = "1h"
         shell: 'echo {params.ver} > {output}'
 
 
@@ -300,7 +309,7 @@ if sampfilt and minimac_version in ['guess', '3']:
         threads: 8
         resources:
             mem_mb = 2048,
-            runtime: "24h"
+            runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -333,7 +342,7 @@ elif minimac_version in ['guess', '3']:
         threads: 8
         resources:
             mem_mb = 2048,
-            runtime: "24h"
+            runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -365,7 +374,7 @@ elif sampfilt:
         threads: 8
         resources:
             mem_mb = 2048,
-            runtime: "24h"
+            runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -386,7 +395,7 @@ else:
         threads: 8
         resources:
             mem_mb = 2048,
-            runtime: "24h"
+            runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
             r'''
@@ -474,7 +483,7 @@ rule concat_chroms_samp:
     threads: 8
     resources:
         mem_mb = 4096,
-        runtime: "24h"
+        runtime = "24h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools concat --threads 8 {input} | bcftools norm -d none -o {output} -Oz"
 
@@ -496,7 +505,7 @@ rule merge_samples_chrom:
     threads: 8
     resources:
         mem_mb = 16000,
-        runtime: "36h"
+        runtime = "36h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools merge -m none --threads 8 {input.vcf} | bcftools norm -d none -o {output} -Oz"
 
@@ -506,7 +515,7 @@ rule concat_chroms_all:
     threads: 8
     resources:
         mem_mb = 2048,
-        runtime: "24h"
+        runtime =  "24h"
     conda: "envs/bcftools.yaml"
     shell: "bcftools concat -o {output} -Oz --threads 8 {input}"
 
@@ -519,7 +528,7 @@ rule make_plink_all:
     threads: 10
     resources:
         mem_mb = 30000,
-        runtime: "96h"
+        runtime = "96h"
     conda: "envs/plink.yaml"
     shell:
         "plink --keep-allele-order --vcf {input} {params.ID} --memory 20000 --threads 10 --make-bed "
@@ -534,7 +543,7 @@ rule make_plink_samp:
     threads: 10
     resources:
         mem_mb = 20000,
-        runtime: "2h"
+        runtime = "2h"
     conda: "envs/plink.yaml"
     shell:
         "plink --keep-allele-order --vcf {input} {params.ID} --memory 20000 --threads 10 --make-bed "
@@ -542,3 +551,29 @@ rule make_plink_samp:
 
 # If bgen outputs are requested
 include: "rules/bgen.smk"
+
+if "fix_fam" in config and config["fix_fam"]:
+    rule fix_fam:
+        input:
+            oldfam = config["fix_fam"],
+            newfam = '{impute_dir}/data/{cohorts}_chrall_filtered.fam'
+        output: "{impute_dir}/data/{cohorts}_chrall_filtered_fixed.fam"
+        threads: 1
+        resources:
+            mem_mb = 1024,
+            time_min = 180
+        conda: "envs/r.yaml"
+        script: 'scripts/fix_fam.R'
+    
+    rule link_fix_bedbim:
+        input:
+            bed = '{impute_dir}/data/{cohorts}_chrall_filtered.bed',
+            bim = '{impute_dir}/data/{cohorts}_chrall_filtered.bim'
+        output:
+            bed = '{impute_dir}/data/{cohorts}_chrall_filtered_fixed.bed',
+            bim = '{impute_dir}/data/{cohorts}_chrall_filtered_fixed.bim'
+        localrule: True
+        shell: '''
+    ln -rs {input.bed} {output.bed}
+    ln -rs {input.bim} {output.bim}
+    '''
diff --git a/workflow/rules/bgen.smk b/workflow/rules/bgen.smk
index 5b2d80f..6987dda 100644
--- a/workflow/rules/bgen.smk
+++ b/workflow/rules/bgen.smk
@@ -8,7 +8,7 @@ rule make_bgen:
     threads: 1
     resources:
         mem_mb = 4000,
-        runtime: "24h"
+        runtime = "24h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -26,7 +26,7 @@ rule cat_bgen_samp:
     threads: 1
     resources:
         mem_mb = 5000,
-        runtime: "120h"
+        runtime = "120h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -48,7 +48,7 @@ rule make_bgen_allsamp:
     threads: 10
     resources:
         mem_mb = 40000,
-        runtime: "24h"
+        runtime = "24h"
     container: 'docker://befh/bgen:v1.1.7'
     shell:
         """
@@ -65,6 +65,6 @@ rule cat_bgen_allsamp:
     threads: 1
     resources:
         mem_mb = 5000,
-        runtime: "120h"
+        runtime = "120h"
     container: 'docker://befh/bgen:v1.1.7'
     shell: "cat-bgen -g {input.gen} -og {output.gen}; cp {input.samp} {output.samp}"

From a0088a9b4a0ae41e199ced868223598d60e19c4e Mon Sep 17 00:00:00 2001
From: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Date: Fri, 6 Jun 2025 17:17:03 -0400
Subject: [PATCH 3/6] full ability to fix fams

---
 workflow/Snakefile                |  8 ++---
 workflow/envs/detect_minimac.yaml |  3 +-
 workflow/scripts/fix_fam.R        | 53 +++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+), 5 deletions(-)
 create mode 100644 workflow/scripts/fix_fam.R

diff --git a/workflow/Snakefile b/workflow/Snakefile
index d1ae365..c06d494 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -308,7 +308,7 @@ if sampfilt and minimac_version in ['guess', '3']:
             sf = sampfilt
         threads: 8
         resources:
-            mem_mb = 2048,
+            mem_mb = 4096,
             runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
@@ -341,7 +341,7 @@ elif minimac_version in ['guess', '3']:
             filt = qualfilt
         threads: 8
         resources:
-            mem_mb = 2048,
+            mem_mb = 4096,
             runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
@@ -373,7 +373,7 @@ elif sampfilt:
             sf = sampfilt
         threads: 8
         resources:
-            mem_mb = 2048,
+            mem_mb = 4096,
             runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
@@ -394,7 +394,7 @@ else:
             filt = qualfilt
         threads: 8
         resources:
-            mem_mb = 2048,
+            mem_mb = 4096,
             runtime = "24h"
         conda: "envs/bcftools.yaml"
         shell:
diff --git a/workflow/envs/detect_minimac.yaml b/workflow/envs/detect_minimac.yaml
index ab49ed7..a570ee5 100644
--- a/workflow/envs/detect_minimac.yaml
+++ b/workflow/envs/detect_minimac.yaml
@@ -1,5 +1,6 @@
 channels:
     - conda-forge
+    - bioconda
 dependencies:
     - python=3.11
-    - pysam=0.22.0
+    - pysam=0.23.1
diff --git a/workflow/scripts/fix_fam.R b/workflow/scripts/fix_fam.R
new file mode 100644
index 0000000..d61a503
--- /dev/null
+++ b/workflow/scripts/fix_fam.R
@@ -0,0 +1,53 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library(dplyr))
+library(vroom)
+library(tidyr)
+library(purrr)
+
+if (!exists("snakemake")) {
+  setClass("snakemake_fake", representation(
+    params = "list", input = "list", output = "list",
+    log = "list", wildcards = "list"))
+  snakemake <- new("snakemake_fake",
+    input = list(
+      oldfam = c("temp/raw/GSA1-AD1_single-probe.fam",
+                 "temp/raw/GSA1-AD2_single-probe.fam",
+                 "temp/raw/GSA1-PD1_single-probe.fam",
+                 "temp/raw/GSA1-PD2_single-probe.fam"),
+      newfam = "temp/raw/raw.fam"
+    ),
+    params = list(),
+    log = list(),
+    output = list("results/raw/raw.fam"),
+    wildcards = list()
+  )
+}
+
+col.n <- c("FID", "IID", "PID", "MID", "Sex", "Phe")
+col.nn <- c("none", "FIDIID", "PID_new", "MID_new", "Sex_new", "Phe_new")
+col.t <- "ccccii"
+
+new_fam <- snakemake@input[["newfam"]] %>%
+  vroom::vroom(col_names = col.nn, col_types = col.t)
+
+stopifnot(nrow(distinct(new_fam, FIDIID)) == nrow(new_fam))
+
+old_fam <- snakemake@input[["oldfam"]] %>%
+  map_dfr(vroom::vroom, col_names = col.n, col_types = col.t) %>%
+  unite("FIDIID", FID, IID, sep = "_", remove = F) %>%
+  distinct(FIDIID, .keep_all = TRUE)
+
+stopifnot(nrow(distinct(old_fam, FIDIID)) == nrow(old_fam))
+
+left_join(new_fam, old_fam, by = "FIDIID") %>%
+  mutate(FID = ifelse(is.na(FID), FIDIID, FID)) %>%
+  mutate(IID = ifelse(is.na(IID), FIDIID, IID)) %>%
+  mutate(PID = ifelse(is.na(PID), PID_new, PID)) %>%
+  mutate(MID = ifelse(is.na(MID), MID_new, MID)) %>%
+  mutate(Sex = ifelse(is.na(Sex), Sex_new, Sex)) %>%
+  mutate(Phe = ifelse(is.na(Phe), Phe_new, Phe)) %>%
+  select(!!col.n) %>%
+  mutate(IID = gsub("�", "", IID)) %>%
+  vroom::vroom_write(snakemake@output[[1]], col_names = F, delim = "\t",
+                     quote = "none")

From 1347bcee432e96e440838779cba69061e56823fd Mon Sep 17 00:00:00 2001
From: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Date: Sun, 22 Feb 2026 16:38:14 -0500
Subject: [PATCH 4/6] fix: more memory for indexing

---
 workflow/Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index c06d494..c11556d 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -493,7 +493,7 @@ rule index_samples_chrom:
     conda: "envs/bcftools.yaml"
     threads: 1
     resources:
-        mem_mb = 256,
+        mem_mb = 1024,
         time_min = 120
     shell: "bcftools index -t {input}"
 

From cd687198124b19c386331592ebf3c2cfcb317168 Mon Sep 17 00:00:00 2001
From: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Date: Mon, 23 Feb 2026 12:06:38 -0500
Subject: [PATCH 5/6] feat: allow merged VCF to be temporary if calling
 pipeline is making further changes when using as module

---
 workflow/Snakefile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index c11556d..baf8ad6 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -509,9 +509,15 @@ rule merge_samples_chrom:
     conda: "envs/bcftools.yaml"
     shell: "bcftools merge -m none --threads 8 {input.vcf} | bcftools norm -d none -o {output} -Oz"
 
+def tempif_cca(path):
+    if config.get("temp_ccs", False):
+        return temp(path)
+    else:
+        return path
+
 rule concat_chroms_all:
     input: expand("{{impute_dir}}/data/by_chrom/all_chr{chrom}_filtered.vcf.gz", chrom=CHROM)
-    output: "{impute_dir}/data/all_chrall_filtered.vcf.gz"
+    output: tempif_cca("{impute_dir}/data/all_chrall_filtered.vcf.gz")
     threads: 8
     resources:
         mem_mb = 2048,

From eafcaf5ad40c1e658004c45248098b23dd8e7766 Mon Sep 17 00:00:00 2001
From: adad <adad@li04e04.chimera.hpc.mssm.edu>
Date: Fri, 24 Apr 2026 13:48:45 -0400
Subject: [PATCH 6/6] fix: deal with single cohort and merge, and remove
 deprecated files

---
 cluster.yaml       | 63 ----------------------------------------------
 lsf.yaml           |  2 --
 workflow/Snakefile | 11 ++++++--
 3 files changed, 9 insertions(+), 67 deletions(-)
 delete mode 100755 cluster.yaml
 delete mode 100644 lsf.yaml

diff --git a/cluster.yaml b/cluster.yaml
deleted file mode 100755
index 30de026..0000000
--- a/cluster.yaml
+++ /dev/null
@@ -1,63 +0,0 @@
-__default__:
-  project: acc_LOAD
-  partition: 'bode'
-  queue: premium
-  cores: 8
-  mem: 2000
-  time: '2:00'
-stats:
-  mem: 6000
-  cores: 22
-  time: '8:00'
-filters: #preparation: #filters:
-  time: '24:00'
-  mem: 128
-fixheaders:
-  cores: 1
-  time: "24:00"
-vcf_merge:
-  time: "36:00"
-rename:
-  mem: 128
-  time: '45'
-  cores: 1
-renameAuto:
-  mem: 1024
-  time: '45'
-  cores: 1
-index_samples_chrom:
-  mem: 256
-  cores: 1
-concat_chroms_all:
-  time: '24:00'
-  mem: 256
-concat_chroms_samp:
-  time: '24:00'
-  mem: 256
-make_bgen:
-  time: "24:00"
-  cores: 1
-make_bgen_allsamp:
-  time: "24:00"
-  cores: 1
-make_gen:
-  time: "36:00"
-  mem: 1000
-  cores: 10
-merge_samples_chrom:
-  time: "36:00"
-cat_bgen_samp:
-  time: "120:00"
-  cores: 1
-  mem: 5000
-cat_bgen_allsamp:
-  time: "120:00"
-  cores: 1
-  mem: 5000
-make_plink_all:
-  mem: 3000
-  cores: 10
-  time: "6:00"
-make_plink_samp:
-  mem: 1000
-  cores: 10
diff --git a/lsf.yaml b/lsf.yaml
deleted file mode 100644
index aebd1be..0000000
--- a/lsf.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-stats:
-  - "-R 'himem'"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index baf8ad6..9e3ef64 100755
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -226,7 +226,7 @@ rule stats:
     conda: "envs/r_stats.yaml"
     threads: 22
     resources:
-        mem_mb = 176000,
+        mem = "256GB",
         runtime = "8h"
     script: "scripts/Post_imputation.Rmd"
 
@@ -507,7 +507,14 @@ rule merge_samples_chrom:
         mem_mb = 16000,
         runtime = "36h"
     conda: "envs/bcftools.yaml"
-    shell: "bcftools merge -m none --threads 8 {input.vcf} | bcftools norm -d none -o {output} -Oz"
+    shell:
+        """
+if [ $(echo {input.vcf} | wc -w) -eq 1 ]; then
+    cp {input.vcf} {output}
+else
+    bcftools merge -m none --threads 8 {input.vcf} | bcftools norm -d none -o {output} -Oz
+fi
+"""
 
 def tempif_cca(path):
     if config.get("temp_ccs", False):