Mercurial > repos > chrisw > monorail_test
changeset 37:5656cfea6d97 draft
Uploaded
author | chrisw |
---|---|
date | Wed, 20 Nov 2019 02:42:57 +0000 |
parents | ad4b5855143b |
children | 318bff30468a |
files | Snakefile monorail.xml |
diffstat | 2 files changed, 12 insertions(+), 13 deletions(-) [+] |
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--- 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
--- 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. -->