hotfix

mv-lab · Aug 28, 2019 · ffa96d6 · ffa96d6
1 parent 57043f0
commit ffa96d6
Showing 33 changed files with 1,335 additions and 4,680 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,15 @@
 # ignore .snakemake
 .snakemake/
+
+command
+
+# ignore mock data (backup)
+mockdata/
+
+# PyCache
+
+.*__pycache__
+
+# rawdata
+
+rawdata/
diff --git a/Snakefile b/Snakefile
@@ -1,18 +1,22 @@
 
-include: "rules/common.smk"
+include: "rules/common.rules.smk"
 
 ##### Modules #####
 
-include: "rules/denovo.smk"
-include: "rules/readqc.smk"
-include: "rules/mapping.smk"
-include: "rules/calling.smk"
+include: "rules/denovo.rules.smk"
+include: "rules/readqc.rules.smk"
+include: "rules/align.rules.smk"
+include: "rules/varcall.rules.smk"
+include: "rules/stats.rules.smk"
+include: "rules/abra2.rules.smk"
 
 ##### Target rules #####
 
 rule all:
     input:
-        rules.denovo.input,
+        #rules.denovo.input,
         rules.reads.input,
         rules.align.input,
+        rules.abra2.output,
         rules.varcall.input,
+        #rules.stats.input,
diff --git a/dag.svg b/dag.svg
diff --git a/data/samplelists/test.txt b/data/samplelists/test.txt
diff --git a/envs/abra2.jar b/envs/abra2.jar
diff --git a/condaenv.yml → envs/condaenv.yml b/condaenv.yml → envs/condaenv.yml
@@ -10,3 +10,5 @@ dependencies:
   - bcftools
   - qualimap
   - AdapterRemoval
+  - seqhax
+  - pigz
diff --git a/rawdata/reference/genome.fa b/rawdata/reference/genome.fa
diff --git a/rawdata/reference/genome.fa.amb b/rawdata/reference/genome.fa.amb
diff --git a/rawdata/reference/genome.fa.ann b/rawdata/reference/genome.fa.ann
diff --git a/rawdata/reference/genome.fa.bwt b/rawdata/reference/genome.fa.bwt
diff --git a/rawdata/reference/genome.fa.fai b/rawdata/reference/genome.fa.fai
diff --git a/rawdata/reference/genome.fa.pac b/rawdata/reference/genome.fa.pac
diff --git a/rawdata/reference/genome.fa.sa b/rawdata/reference/genome.fa.sa
diff --git a/rawdata/runs/run_1/A.fastq.gz b/rawdata/runs/run_1/A.fastq.gz
diff --git a/rawdata/runs/run_1/B1.fastq.gz b/rawdata/runs/run_1/B1.fastq.gz
diff --git a/rawdata/runs/run_1/B2.fastq.gz b/rawdata/runs/run_1/B2.fastq.gz
diff --git a/rawdata/runs/run_1/C.fastq.gz b/rawdata/runs/run_1/C.fastq.gz
diff --git a/rawdata/runs/run_2/C.fastq.gz b/rawdata/runs/run_2/C.fastq.gz
diff --git a/rules/abra2.rules.smk b/rules/abra2.rules.smk
@@ -0,0 +1,26 @@
+rule abra2:
+    input:
+        bam="data/alignments/sets/bwa~genome~all_samples.bam",
+        #ref= lambda wc: config['refs'][wc.ref],
+    output:
+        "data/abra/bwa~genome~all_samples.bam",
+    log:
+        log = "data/log/bwa~genome.log",
+    threads:
+        3
+    params:
+        region = config['abra2']['regions'],
+        abra_temp = config['abra2']['temp'],
+        abra_release = config['abra2']['release'],
+        mem= config['abra2']['memory'],
+    shell:
+        "( java"
+        "   -{params.mem}"
+        "   -jar {params.abra_release}"
+        "   --in {input.bam}"
+        "   --out {output}"
+        "   --ref rawdata/reference/genome.fa"
+        "   --threads {threads}"
+        "   --targets {params.region}"
+        "   --tmpdir {params.abra_temp}"
+        ") >{log.log} 2>&1"