updating workflow: configs + inti rule + rawdata

mv-lab · Sep 12, 2019 · ceee6e9 · ceee6e9
1 parent 243d42d
commit ceee6e9
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Showing 17 changed files with 20 additions and 1,218 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,9 +6,11 @@ command
 
 # Ignore mock data (backup)
 mockdata/
+oldtoy/
 
 # PyCache
 .*__pycache__
+utils/__pycache__/
 
 # generated data files
 data/
@@ -18,4 +20,5 @@ data/
 rawdata/reference/*
 rawdata/snpeffdata/genomes/*
 
+dag.svg
 toydata/
diff --git a/Snakefile b/Snakefile
@@ -18,6 +18,6 @@ rule all:
         #rules.denovo.input,
         rules.reads.input,
         rules.align.input,
-        #rules.abra2.output,
+        rules.abra2.output,
         rules.varcall.input,
-        #rules.stats.input,
+        rules.stats.input,
diff --git a/runconfig.yml → configs/runconfig.yml b/runconfig.yml → configs/runconfig.yml
diff --git a/toolconfig.yml → configs/toolconfig.yml b/toolconfig.yml → configs/toolconfig.yml
diff --git a/dag.svg b/dag.svg
diff --git a/data/samplelists/all_samples.txt b/data/samplelists/all_samples.txt
@@ -1,3 +1,3 @@
-A
-B
-C
+D2
+D3
+con
diff --git a/data/samplelists/mutants.txt b/data/samplelists/mutants.txt
@@ -1,2 +1,2 @@
-A
-B
+D2
+D3
diff --git a/metadata/sample2runlib.csv b/metadata/sample2runlib.csv
@@ -1,6 +1,5 @@
 run,library,sample,Include
-run_1,A,A,Y
-run_1,B1,B,Y
-run_1,B2,B,Y
-run_1,C,C,Y
-run_2,C,C,Y
+run_1,con,con,Y
+run_1,D2,D2,Y
+run_1,D3,D3,Y
+
diff --git a/metadata/samplesets/mutants.txt b/metadata/samplesets/mutants.txt
@@ -1,2 +1,2 @@
-A
-B
+D2
+D3
diff --git a/metadata/samplesets/well_type.txt b/metadata/samplesets/well_type.txt
diff --git a/metadata/samplesets/wild_type.txt b/metadata/samplesets/wild_type.txt
@@ -0,0 +1 @@
+con
diff --git a/rawdata/runs/run_1/D2.fastq.gz b/rawdata/runs/run_1/D2.fastq.gz
diff --git a/rawdata/runs/run_1/D3.fastq.gz b/rawdata/runs/run_1/D3.fastq.gz
diff --git a/rawdata/runs/run_1/con.fastq.gz b/rawdata/runs/run_1/con.fastq.gz
diff --git a/regions.bed b/regions.bed
diff --git a/rules/init.rules.smk b/rules/init.rules.smk
@@ -5,8 +5,8 @@
 from utils import snkmk
 import os
 
-configfile: "toolconfig.yml"
-configfile: "runconfig.yml"
+configfile: "configs/toolconfig.yml"
+configfile: "configs/runconfig.yml"
 report: "../report/workflow.rst"
 
 

diff --git a/rules/readqc.rules.smk b/rules/readqc.rules.smk
@@ -28,7 +28,7 @@ rule reads:
 
 ##### Actual rules #####
 
-ruleorder: qcreads > qcreads_il
+ruleorder: qcreads_il > qcreads
 rule qcreads:
     input:
         r1="rawdata/runs/{run}/{lib}_R1.fastq.gz",
-Original file line number
+Diff line change
@@ -1,3 +1,3 @@
-    A
-    B
-    C
+    D2
+    D3
+    con