Commit 3d3fdb83 authored by Curtis Hendrickson's avatar Curtis Hendrickson
Browse files

refactor to put aligner versions in variables.

parent a73166b5
# editor files
*~
\#*
# snakemake temp
.snakemake
...@@ -15,7 +15,11 @@ NCBI = NCBIRemoteProvider(email=my_NCBI_Email) # email required by NCBI to preve ...@@ -15,7 +15,11 @@ NCBI = NCBIRemoteProvider(email=my_NCBI_Email) # email required by NCBI to preve
cov2acc="NC_045512.2" cov2acc="NC_045512.2"
cov2abbrev="cov2WuHan1" 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: rule all:
input: input:
...@@ -24,19 +28,19 @@ rule all: ...@@ -24,19 +28,19 @@ rule all:
# samtools faidx # samtools faidx
,Idx=expand("{strain}/{genome}.{ext}",strain=[cov2abbrev],genome=[cov2acc],ext=["fasta.fai"]) #,"dict"]) ,Idx=expand("{strain}/{genome}.{ext}",strain=[cov2abbrev],genome=[cov2acc],ext=["fasta.fai"]) #,"dict"])
# star index # 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 # bwa index
# MISSING - liamvdp did by hand # 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 (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: AGAT_gff2gtf > AGAT_gff2ext_cleaner > gunzip
ruleorder: gtf_get_rRNA_gene_list > gunzip ruleorder: gtf_get_rRNA_gene_list > gunzip
rule gunzip: rule gunzip:
wildcard_constraints: file=".+(?<!gz)" # not ends with gz wildcard_constraints: file=".+(?<!gz)" # not ends with gz
output: "x{dir}/{file}" output: "{dir}/{file}"
input: "{dir}/{file}.gz" input: "{dir}/{file}.gz"
shell: "gunzip -c '{input}' > '{output}'" shell: "gunzip -c '{input}' > '{output}'"
...@@ -113,18 +117,18 @@ rule AGAT_gff2ext_cleaner: ...@@ -113,18 +117,18 @@ rule AGAT_gff2ext_cleaner:
# ---------------------------------------------------------------------- # ----------------------------------------------------------------------
rule STAR_index_genome_with_gtf: rule STAR_index_genome_with_gtf:
output: 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"]) index_file=["SAindex", "SA", "Genome", "sjdbInfo.txt"])
input: input:
fa="{strain}/{genome}.fasta", fa="{strain}/{genome}.fasta",
gtf="{strain}/{genome}.gtf" gtf="{strain}/{genome}.gtf"
# MUST match that from CCTS-Informatics-Pipelines / Snakemake-Eukaryotic-RNAseq-Pipeline # 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. # 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 threads: 12
log: log:
stdout="{strain}/{genome}/STAR/STAR_2.5.3a-{overhang}/log_{overhang}_stdout.txt" stdout="{strain}/{genome}/STAR/STAR_{align_ver}-{overhang}/log_{overhang}_stdout.txt"
, stderr="{strain}/{genome}/STAR/STAR_2.5.3a-{overhang}/log_{overhang}_stderr.txt" , stderr="{strain}/{genome}/STAR/STAR_{align_ver}a-{overhang}/log_{overhang}_stderr.txt"
shell: shell:
"STAR " "STAR "
" --runThreadN {threads} " " --runThreadN {threads} "
...@@ -235,9 +239,9 @@ rule minimap2: ...@@ -235,9 +239,9 @@ rule minimap2:
rule minimap2_index_preset: rule minimap2_index_preset:
input: fa="{strain}/{genome}.fasta" 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 threads: 3
conda: "envs/minimap2_2.17.yaml" conda: "envs/minimap2_{align_ver}.yaml"
shell: shell:
"minimap2 " "minimap2 "
" -t {threads} " " -t {threads} "
......
name: minimap2
channels:
- bioconda
- defaults
dependencies:
- minimap2=2.17
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