workflow v1.6

+ new release! + fixed bugs: generate files, paths etc + new metadata with cohort + snpeff works + test with 2 references
mv-lab · Oct 14, 2019 · 9819eb5 · 9819eb5
1 parent 3e225d0
commit 9819eb5
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Showing 37 changed files with 725 additions and 511 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,20 +2,12 @@
 .snakemake/
 */.snakemake.*
 
-# Ignore notes, txt etc
-command
-
 # PyCache
 */__pycache__
 
 # generated data files
-data/*
-!data/readme
-log/
-plots/
+output/*
+!output/readme
 
 # rawdata (size problem)
-#rawdata/reference/*
-#rawdata/snpeffdata/genomes/*
-rawdata/snpeffdata/*
 genomes_and_annotations/snpeffdata/
diff --git a/Snakefile b/Snakefile
@@ -19,3 +19,4 @@ rule all:
         rules.align.input,
         rules.varcall.input,
         rules.stats.input,
+        rules.snpeff.output,
diff --git a/configs/toolconfig.yml → config.yml b/configs/toolconfig.yml → config.yml
@@ -1,6 +1,20 @@
 
 samples: "metadata/sample2runlib.csv"
 
+sample_sets: []
+
+refs:
+  Sorghum_bicolor_NCBIv3.42: genomes_and_annotations/Sorghum_bicolor_NCBIv3.42/Sorghum_bicolor_NCBIv3.42.fa
+  Sorghum: genomes_and_annotations/Sorghum/Sorghum.fa
+
+snpeff:
+  name: Sorghum_bicolor_NCBIv3.42
+  #Sorghum_bicolor_NCBIv3.42: genomes_and_annotations/Sorghum/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.42.gtf.gz
+  filter: strict
+
+# Path to any database of known variants, ideally as it is provided by the GATK bundle.
+# known-variants: genomes_and_annotations/Sorghum/Sbicolor_Patterson_454.vcf.gz
+
 qc:
   _DEFAULT_:
     adapter1: CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
@@ -11,39 +25,42 @@ qc:
     adapter2: CTGTCTCTTATACACATCTGACGCTGCCGACGANNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT
     minqual: 25
 
-sample_sets: []
-
-
-refs:
-  Sorghum: genomes_and_annotations/genomes/Sorghum/genome.fa
-
 
 mapping:
   aligners:
     - bwa
   refs:
-    - Sorghum
+    - Sorghum_bicolor_NCBIv3.42
   samplesets:
     - all_samples
   ngm:
     sensitivity: 0.5
 
 
-snpeff:
-  name: Sorghum_bicolor_NCBIv3.42
-  Sorghum: genomes_and_annotations/snpeffdata/genomes/Sorghum_bicolor_NCBIv3.42.fa.gz
+abra2:
+  memory:
+    - Xmx6g
+  release:
+    - envs/abra2.jar
+  temp:
+    - /tmp
+  threads:
+    - 10
+  regions:
+    - metadata/contigs_of_interest.bed
 
 
 denovodist:
   kwip_sketchsize: 1e9
   mash_sketchsize: 1e5
   sourmash_sketchsize: 1e5
   ksize: 21
-  kwip_sets: [] 
+  kwip_sets: []
   mash_sets: # we can subset from everything for (sour)mash
     - all_samples
   sourmash_sets: []
 
+
 varcall:
   minmapq:
     bwa: 30
@@ -54,10 +71,10 @@ varcall:
   aligners:
     - bwa
   callers:
-    #- mpileup
+    - mpileup
     - freebayes
   refs:
-    - Sorghum
+    - Sorghum_bicolor_NCBIv3.42
   samplesets:
     - all_samples
   filters:

diff --git a/configs/runconfig.yml b/configs/runconfig.yml
diff --git a/data/readme b/data/readme
diff --git a/data/samplelists/GENERATED_FILES_DO_NOT_EDIT b/data/samplelists/GENERATED_FILES_DO_NOT_EDIT
diff --git a/data/samplelists/all_samples.txt b/data/samplelists/all_samples.txt