refactor to put aligner versions in variables.

.gitignore

+# editor files
+*~
+\#*
+# snakemake temp
+.snakemake

Snakefile

@@ -15,7 +15,11 @@ NCBI = NCBIRemoteProvider(email=my_NCBI_Email) # email required by NCBI to preve
 cov2acc="NC_045512.2"
 cov2abbrev="cov2WuHan1"
 
-MINIMAP2_PRESETS=["map-ont","map-pb","asm5"]
+MINIMAP2_PRESETS=["map-ont","map-pb","asm5","asm20"]
+
+STAR_VERS=["2.5.3a"]
+BWA_VERS=["0.7.17"]
+MINIMAP2_VERS=["2.17"]
 
 rule all:
     input: 
@@ -24,19 +28,19 @@ rule all:
         # samtools faidx
         ,Idx=expand("{strain}/{genome}.{ext}",strain=[cov2abbrev],genome=[cov2acc],ext=["fasta.fai"]) #,"dict"]) 
         # star index
-        ,StarIDX=expand("{strain}/{genome}/STAR/STAR_2.5.3a-{overhang}/{index_file}",strain=[cov2abbrev],genome=[cov2acc],overhang=["100"],index_file=["SAindex"]) 
+        ,StarIDX=expand("{strain}/{genome}/STAR/STAR_{align_ver}-{overhang}/{index_file}",strain=[cov2abbrev],genome=[cov2acc],overhang=["100"],index_file=["SAindex"],align_ver=STAR_VERS) 
         # bwa index
         # MISSING - liamvdp did by hand
-        ,BWAIdx=expand("{strain}/BWA/0.7.17/{genome}.{ext}",strain=[cov2abbrev],genome=[cov2acc],ext=["fasta.fai","fasta.bwt","fasta.sa"])#, "dict"]) 
+        ,BWAIdx=expand("{strain}/BWA/{bwa_ver}/{genome}.{ext}",strain=[cov2abbrev],genome=[cov2acc],ext=["fasta.fai","fasta.bwt","fasta.sa"],bwa_ver=BWA_VERS)#, "dict"]) 
         # minimap2 (ont & pb)
-        ,minimap2=expand("{strain}/minimap2/minimap2_2.17/{preset}/{genome}.mmi", preset=MINIMAP2_PRESETS, strain=[cov2abbrev], genome=[cov2acc] )
+        ,minimap2=expand("{strain}/minimap2/minimap2_{align_ver}/{preset}/{genome}.mmi", preset=MINIMAP2_PRESETS, strain=[cov2abbrev], genome=[cov2acc], align_ver=MINIMAP_VERS )
 
 ruleorder: AGAT_gff2gtf > AGAT_gff2ext_cleaner > gunzip
 ruleorder: gtf_get_rRNA_gene_list > gunzip
 
 rule gunzip:
     wildcard_constraints: file=".+(?<!gz)" # not ends with gz
-    output: "x{dir}/{file}"
+    output: "{dir}/{file}"
     input: "{dir}/{file}.gz"
     shell: "gunzip -c '{input}' > '{output}'"
 
@@ -113,18 +117,18 @@ rule AGAT_gff2ext_cleaner:
 # ----------------------------------------------------------------------
 rule STAR_index_genome_with_gtf:
     output: 
-        expand("{{strain}}/{{genome}}/STAR/STAR_2.5.3a-{{overhang}}/{index_file}",
+        expand("{{strain}}/{{genome}}/STAR/STAR_{align_ver}-{{overhang}}/{index_file}",
             index_file=["SAindex", "SA", "Genome", "sjdbInfo.txt"])
     input: 
         fa="{strain}/{genome}.fasta",
         gtf="{strain}/{genome}.gtf"
     # MUST match that from CCTS-Informatics-Pipelines / Snakemake-Eukaryotic-RNAseq-Pipeline
     # which comes from a plug-in. We grabbed the yaml file from .snakemake/conda/8a33389f.yaml after a run.
-    conda: "envs/STAR_2.5.3a.yaml"
+    conda: "envs/STAR_{align_ver}.yaml"
     threads: 12
     log: 
-        stdout="{strain}/{genome}/STAR/STAR_2.5.3a-{overhang}/log_{overhang}_stdout.txt"
-        , stderr="{strain}/{genome}/STAR/STAR_2.5.3a-{overhang}/log_{overhang}_stderr.txt"
+        stdout="{strain}/{genome}/STAR/STAR_{align_ver}-{overhang}/log_{overhang}_stdout.txt"
+        , stderr="{strain}/{genome}/STAR/STAR_{align_ver}a-{overhang}/log_{overhang}_stderr.txt"
     shell: 
         "STAR "
         "    --runThreadN {threads} "
@@ -235,9 +239,9 @@ rule minimap2:
          
 rule minimap2_index_preset:
     input: fa="{strain}/{genome}.fasta"
-    output: mmi="{strain}/minimap2/minimap2_2.17/{preset}/{genome}.mmi"
+    output: mmi="{strain}/minimap2/minimap2_{align_ver}/{preset}/{genome}.mmi"
     threads: 3
-    conda: "envs/minimap2_2.17.yaml"
+    conda: "envs/minimap2_{align_ver}.yaml"
     shell: 
         "minimap2 "
         " -t {threads} "

envs/minimap2_2.17.yaml

+name: minimap2
+channels:
+  - bioconda
+  - defaults
+dependencies:
+  - minimap2=2.17