Mercurial > repos > chrisw > monorail_test
changeset 35:e4dc3d0c31de draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 20 Nov 2019 00:44:24 +0000 |
| parents | 358a1cf83b7b |
| children | ad4b5855143b |
| files | Snakefile monorail.xml |
| diffstat | 2 files changed, 13 insertions(+), 11 deletions(-) [+] |
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--- 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:
--- 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"/>