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Merge pull request #119 from Hammarn/master
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minor RSEQC bugfix
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ewels authored Apr 21, 2017
2 parents a93015a + 2b62569 commit d868734
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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# NGI-RNAseq
## [1.0.4](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.0.3) - 2017-04-21
RseQC hotfix, input file was not supplied properly to one of the scripts

## [1.0.3](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.0.1) - 2017-04-19
## [1.0.3](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.0.3) - 2017-04-19
Hotfix to fix minor bug affecting strandedness for StringTie run.

## [1.0.2](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.0.2) - 2017-04-11
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5 changes: 3 additions & 2 deletions main.nf
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Expand Up @@ -22,7 +22,7 @@ vim: syntax=groovy
*/

// Pipeline version
version = '1.0.3'
version = '1.0.4'

// Configurable variables
params.project = false
Expand Down Expand Up @@ -584,6 +584,7 @@ process rseqc {
else if (filename.indexOf("inner_distance.txt") > 0) "inner_distance/$filename"
else if (filename.indexOf("inner_distance_freq.txt") > 0) "inner_distance/data/$filename"
else if (filename.indexOf("inner_distance_plot.r") > 0) "inner_distance/rscripts/$filename"
else if (filename.indexOf("inner_distance_plot.pdf") > 0) "inner_distance/plots/$filename"
else if (filename.indexOf("junction_plot.r") > 0) "junction_annotation/rscripts/$filename"
else if (filename.indexOf("junction.xls") > 0) "junction_annotation/data/$filename"
else if (filename.indexOf("splice_events.pdf") > 0) "junction_annotation/events/$filename"
Expand Down Expand Up @@ -616,7 +617,7 @@ process rseqc {
bam_stat.py -i $bam_rseqc 2> ${bam_rseqc.baseName}.bam_stat.txt
junction_saturation.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12 2> ${bam_rseqc.baseName}.junction_annotation_log.txt
inner_distance.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12
geneBody_coverage.py -i ${bam_rseqc.baseName} -o ${bam_rseqc.baseName}.rseqc -r $bed12
geneBody_coverage.py -i $bam_rseqc -o ${bam_rseqc.baseName}.rseqc -r $bed12
read_distribution.py -i $bam_rseqc -r $bed12 > ${bam_rseqc.baseName}.read_distribution.txt
read_duplication.py -i $bam_rseqc -o ${bam_rseqc.baseName}.read_duplication
echo "Filename $bam_rseqc RseQC version: "\$(read_duplication.py --version)
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