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
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} "
......
name: minimap2
channels:
- bioconda
- defaults
dependencies:
- minimap2=2.17
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