separated samtools, bcftools and realign envs to avoid conflicts

ylab-hi · Jun 22, 2024 · ee09756 · ee09756
1 parent 9df2e17
commit ee09756
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Prioritization of neoantigens is now done separately for each variant type (speeds up the process)
 - NMD information (e.g., escape rule,...) is now also calculated for all variants
 
+## [0.2.7] - 2024-06-23 
+
+### Fix 
+
+- Separated samtools, bcftools and realign environments to avoid conflicts
+
 ## [0.2.6] - 2024-06-20
 
 ### Fix 

diff --git a/workflow/envs/bcftools.yml b/workflow/envs/bcftools.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bcftools=1.20
diff --git a/workflow/envs/realign.yml b/workflow/envs/realign.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bwa=0.7.18
+  - samtools=1.20
diff --git a/workflow/envs/samtools.yml b/workflow/envs/samtools.yml
@@ -1,6 +1,6 @@
 channels:
+  - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
- - samtools=1.9
- - bcftools=1.9
-
+ - samtools=1.14
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -201,7 +201,7 @@ rule realign:
   output:
     bam="results/{sample}/{seqtype}/align/{group}_final_BWA.bam",
   conda:
-    "../envs/basic.yml"
+    "../envs/realign.yml"
   log:
     "logs/{sample}/realign/{seqtype}_{group}.log"
   threads: config['threads']
@@ -225,7 +225,7 @@ if config['data']['dnaseq_filetype'] in ['.fq','.fastq']:
     log:
       "logs/{sample}/bwa_align/dnaseq_{group}.log"
     conda:
-      "../envs/basic.yml"
+      "../envs/realign.yml"
     params:
       extra=""
     threads: config['threads']

diff --git a/workflow/rules/all.smk b/workflow/rules/all.smk
diff --git a/workflow/rules/altsplicing.smk b/workflow/rules/altsplicing.smk
@@ -54,7 +54,7 @@ rule sort_altsplicing:
   log:
     "logs/{sample}/spladder/{group}_sort.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -70,7 +70,7 @@ rule combine_altsplicing:
   log:
     "logs/{sample}/exitrons/combine_exitrons.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat --naive -O z {input} -o  - | bcftools sort -O z -o {output} > {log} 2>&1

diff --git a/workflow/rules/custom.smk b/workflow/rules/custom.smk
@@ -28,7 +28,7 @@ rule sort_custom_variants:
   log:
     "logs/{sample}/custom/sort_custom_variants.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1

diff --git a/workflow/rules/exitron.smk b/workflow/rules/exitron.smk
@@ -116,7 +116,7 @@ rule sort_exitron:
   log:
     "logs/exitron_sort_{sample}_{group}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -132,7 +132,7 @@ rule combine_exitrons:
   log:
     "logs/{sample}/exitrons/combine_exitrons.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat --naive -O z {input} -o  - | bcftools sort -O z -o {output} > {log} 2>&1

diff --git a/workflow/rules/germline.smk b/workflow/rules/germline.smk
@@ -97,7 +97,7 @@ rule sort_variants_htc_first_round:
   log:
     "logs/{sample}/gatk/haplotypecaller/{seqtype}_{group}_1rd_{chr}_sort.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -113,7 +113,7 @@ rule index_variants_htc_first_round:
   log:
      "logs/{sample}/gatk/haplotypecaller/{seqtype}_{group}_1rd_{chr}_index.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1
@@ -130,7 +130,7 @@ rule merge_variants_htc_first_round:
   log:
     "logs/{sample}/gatk/haplotypecaller/{seqtype}_{group}_1rd_merge.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat -O z -a {input.vcf} -o {output} > {log} 2>&1
@@ -146,7 +146,7 @@ rule index_merged_variants_htc_first_round:
   log:
     "logs/{sample}/gatk/haplotypecaller/{seqtype}_{group}_1rd_index.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1
@@ -346,7 +346,7 @@ rule sort_variants_htc_final_round:
   log:
     "logs/{sample}/indel/gatk/haplotypecaller/sort_final_{seqtype}_{group}_{chr}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -362,7 +362,7 @@ rule index_variants_htc_final_round:
   log:
      "logs/{sample}/indel/gatk/haplotypecaller/index_final_{seqtype}_{group}_{chr}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1
@@ -379,7 +379,7 @@ rule merge_variants_htc_final_round:
   log:
     "logs/{sample}/indel/gatk/haplotypecaller/merge_final_{seqtype}_{group}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat -O z -a {input.vcf} -o {output} > {log} 2>&1
@@ -395,7 +395,7 @@ rule index_merged_variants_htc_final_round:
   log:
     "logs/{sample}/indel/gatk/haplotypecaller/index_final_{seqtype}_{group}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1

diff --git a/workflow/rules/indel.smk b/workflow/rules/indel.smk
@@ -110,7 +110,7 @@ rule longindel_sort_and_compress:
   log:
     "logs/{sample}/transindel/{seqtype}_{group}_longindel_sort.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -126,7 +126,7 @@ rule combine_longindels:
   log:
     "logs/{sample}/transindel/combine_longindels.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat --naive -O z {input} -o - | bcftools sort -O z -o {output} > {log} 2>&1
@@ -222,7 +222,7 @@ rule sort_short_indels_m2:
   log:
     "logs/{sample}/gatk/mutect2/sort_{seqtype}_{group}_{chr}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -238,7 +238,7 @@ rule index_short_indels_m2:
   log:
      "logs/{sample}/gatk/mutect2/index_{seqtype}_{group}_{chr}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1
@@ -255,7 +255,7 @@ rule merge_short_indels_m2:
   log:
     "logs/{sample}/gatk/mutect2/merge_{seqtype}_{group}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat -O z -a {input.vcf} -o {output} > {log} 2>&1
@@ -273,7 +273,7 @@ rule index_merged_short_indels_m2:
   log:
      "logs/{sample}/gatk/mutect2/index_merged_{seqtype}_{group}.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools index -t {input} > {log} 2>&1
@@ -328,7 +328,7 @@ rule sort_aug_short_indels_m2:
   log:
     "logs/{sample}/transindel/{seqtype}_{group}_shortindel_sort.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -344,7 +344,7 @@ rule combine_aug_short_indels_m2:
   log:
     "logs/{sample}/transindel/combine_longindels.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat --naive -O z {input} -o - | bcftools sort -O z -o {output} > {log} 2>&1
@@ -398,7 +398,7 @@ rule sort_somatic_SNVs_m2:
   log:
     "logs/{sample}/transindel/{seqtype}_{group}_SNVs_sort.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools sort {input} -o - | bcftools view -O z -o {output} > {log} 2>&1
@@ -414,7 +414,7 @@ rule combine_somatic_SNVs_m2:
   log:
     "logs/{sample}/transindel/combine_somatic_SNVs.log"
   conda:
-    "../envs/samtools.yml"
+    "../envs/bcftools.yml"
   shell:
     """
       bcftools concat --naive -O z {input} -o - | bcftools sort -O z -o {output} > {log} 2>&1

diff --git a/workflow/rules/postproc.smk b/workflow/rules/postproc.smk