# HG changeset patch
# User chrisw
# Date 1574210664 0
# Node ID e4dc3d0c31ded892bd3863b9aa9706997b3e2be6
# Parent  358a1cf83b7b6375904f204d2c90258b8072fd8d
Uploaded

diff -r 358a1cf83b7b -r e4dc3d0c31de Snakefile
--- a/Snakefile	Tue Nov 19 05:44:09 2019 +0000
+++ b/Snakefile	Wed Nov 20 00:44:24 2019 +0000
@@ -46,7 +46,8 @@
         raise cpe
 
 import re
-STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)')
+#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)')
 def remove_steps_files():
     #modify STEP and FILES
     #so we don't run download or unmapped steps
@@ -175,17 +176,17 @@
 rule make_galaxy_links:
     input: 
         config['output'] + '/{quad}.sjout.zst',
-        config['output'] + '/{quad}.fastq_check.tsv.zst',
+        #config['output'] + '/{quad}.fastq_check.tsv.zst',
         config['output'] + '/{quad}.bamcount_auc.tsv',
-        config['output'] + '/{quad}.bamcount_frag.tsv',
+        #config['output'] + '/{quad}.bamcount_frag.tsv',
         config['output'] + '/{quad}.all.exon_bw_count.zst',
-        config['output'] + '/{quad}.unique.exon_bw_count.zst',
+        #config['output'] + '/{quad}.unique.exon_bw_count.zst',
         config['output'] + '/{quad}.all.bw.zst',
-        config['output'] + '/{quad}.unique.bw.zst',
-        config['output'] + '/{quad}.fastq_check.log',
-        config['output'] + '/{quad}.align.log',
-        config['output'] + '/{quad}.sort.log',
-        config['output'] + '/{quad}.bamcount.log',
+        #config['output'] + '/{quad}.unique.bw.zst',
+        #config['output'] + '/{quad}.fastq_check.log',
+        #config['output'] + '/{quad}.align.log',
+        #config['output'] + '/{quad}.sort.log',
+        #config['output'] + '/{quad}.bamcount.log',
     output:
         config['output'] + '/{quad}.done'
     params:
diff -r 358a1cf83b7b -r e4dc3d0c31de monorail.xml
--- a/monorail.xml	Tue Nov 19 05:44:09 2019 +0000
+++ b/monorail.xml	Wed Nov 20 00:44:24 2019 +0000
@@ -80,9 +80,10 @@
     </inputs>
     <outputs>
         <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>
+        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="SJ.out.tab"/>
+        <data format="bigwig" name="all_bw" label="${tool.name} on ${on_string}: ALL BW" from_work_dir="bamcount_auc.tsv"/>
+        <!-- 
         <data format="txt" name="frag" label="${tool.name} on ${on_string}: Fragment Distribution" from_work_dir="bamcount_frag.tsv"/>
-        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="SJ.out.tab"/>
-        <!-- 
         <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
         <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bc.auc.tsv"/>
         <data format="txt" name="bc_log" label="${tool.name} on ${on_string}: bamcount log" from_work_dir="bc.log"/>