changeset 32:13df910d0683 draft

Uploaded

--- a/Snakefile	Thu Nov 14 07:42:04 2019 +0000
+++ b/Snakefile	Tue Nov 19 03:02:23 2019 +0000
@@ -46,7 +46,7 @@
         raise cpe
 
 import re
-STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)')
+STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)')
 def remove_steps_files():
     #modify STEP and FILES
     #so we don't run download or unmapped steps
@@ -98,15 +98,6 @@
     #create fastq 2 if not paired
     if i == 2:
         open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() 
-    #create expected file structure for annotated exon bed file & reference index
-    #ref = config['ref']
-    #config['ref'] = os.path.abspath('.')
-    #os.makedirs('%s/%s' % (config['ref'], genome))
-    #os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome))
-    #os.makedirs('%s/%s/gtf' % (config['ref'], genome))
-    #os.symlink(config['exon_bed'], 'exons.tmp')
-    #os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed')))
-    #TODO may need to add additional symlinking for HISAT2 unmapped alignments
     return([run_acc, study_acc, genome, method])
 
 
@@ -185,10 +176,8 @@
     input: 
         config['output'] + '/{quad}.sjout.zst',
         config['output'] + '/{quad}.fastq_check.tsv.zst',
-        config['output'] + '/{quad}.bamcount_nonref.csv.zst',
         config['output'] + '/{quad}.bamcount_auc.tsv',
         config['output'] + '/{quad}.bamcount_frag.tsv',
-        config['output'] + '/{quad}.Chimeric.out.junction.zst',
         config['output'] + '/{quad}.all.exon_bw_count.zst',
         config['output'] + '/{quad}.unique.exon_bw_count.zst',
         config['output'] + '/{quad}.all.bw.zst',

--- a/monorail.xml	Thu Nov 14 07:42:04 2019 +0000
+++ b/monorail.xml	Tue Nov 19 03:02:23 2019 +0000
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="2.7.3a">star</requirement>
-        <requirement type="package" version="0.2.6">bamcount</requirement>
+        <requirement type="package" version="0.4.0">bamcount</requirement>
         <requirement type="package" version="5.4.0">snakemake-minimal</requirement>
         <requirement type="package" version="1.3.3">zstd</requirement>
         <requirement type="package" version="1.3">seqtk</requirement>
@@ -80,12 +80,13 @@
     </inputs>
     <outputs>
         <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>
+        <data format="txt" name="frag" label="${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 ${on_string}: bamcount log" from_work_dir="bc.log"/>
         <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"/>
-        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"/>
         <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam"/>
         <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai"/>
         -->

--- a/tool_dependencies.xml	Thu Nov 14 07:42:04 2019 +0000
+++ b/tool_dependencies.xml	Tue Nov 19 03:02:23 2019 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bamcount" version="0.2.6">
-        <repository changeset_revision="f02b4483eda2" name="bamcount_test" owner="chrisw" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="bamcount" version="0.4.0">
+        <repository changeset_revision="cb4c1efac7af" name="bamcount_test" owner="chrisw" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>