# HG changeset patch
# User chrisw
# Date 1574217777 0
# Node ID 5656cfea6d97acf9b954cbce9703524e8aaa0737
# Parent  ad4b5855143bbd26421e30e8396ffc47b144c03e
Uploaded

diff -r ad4b5855143b -r 5656cfea6d97 Snakefile
--- a/Snakefile	Wed Nov 20 00:47:20 2019 +0000
+++ b/Snakefile	Wed Nov 20 02:42:57 2019 +0000
@@ -47,7 +47,7 @@
 
 import re
 #limit the outputs/steps to only 1) STAR called junctions 2) all reads per-base coverage (BigWigs) 3) all reads exon summarized coverage 4) AUC (for QC)
-STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)(fastq_check)|(frag)|(unique)')
+STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)|(fastq_check)|(frag)|(unique)')
 def remove_steps_files():
     #modify STEP and FILES
     #so we don't run download or unmapped steps
diff -r ad4b5855143b -r 5656cfea6d97 monorail.xml
--- a/monorail.xml	Wed Nov 20 00:47:20 2019 +0000
+++ b/monorail.xml	Wed Nov 20 02:42:57 2019 +0000
@@ -17,28 +17,27 @@
     </requirements>
         <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
         <command detect_errors="aggressive"><![CDATA[
-            snakemake --snakefile "$__tool_directory__/Snakefile"
-            -j \${GALAXY_SLOTS:-4} 
-            --config 
+            run_mr_snakemake.sh "$__tool_directory__/Snakefile"
+            \${GALAXY_SLOTS:-4} 
+                    "$index_source.fields.path"
+                    "$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
+                    "."
+                    "./tmp"
+                    "$index_source.fields.name"
                     #if str($singlePaired.sPaired) == "paired_collection"
-                        inputs="$singlePaired.input.forward,$singlePaired.input.reverse"
+                        "$singlePaired.input.forward,$singlePaired.input.reverse"
                         #if $singlePaired.input.forward.is_of_type("fastq.gz"):
-                            compressed=1
+                            "compressed=1"
                         #end if
                     #else
-                        inputs="$singlePaired.input1"
+                        "$singlePaired.input1"
                         #if str($singlePaired.sPaired) == "paired"
                             inputs="$singlePaired.input1,$singlePaired.input2"
                         #end if
                         #if $singlePaired.input1.is_of_type("fastq.gz"):
-                            compressed=1
+                            "compressed=1"
                         #end if
                     #end if
-                    ref="$index_source.fields.path"
-                    exon_bed="$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
-                    genome="$index_source.fields.name"
-                    output="."
-                    temp="./tmp"
     ]]></command>
     <inputs>
  <!-- FASTQ input(s) and options specifically for paired-end data. -->