Unverified Commit 32219490 authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
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Merge pull request #85 from luslab/dev 

1.1 Fixes
parents 810edea7 1e070f9d

CHANGELOG.md

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@@ -43,9 +43,11 @@ We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and everyone i 
* Added pipeline diagram to [[README](https://github.com/nf-core/cutandrun/blob/master/README.md)]

* Upgraded all modules (local and nf-core) to support the new versioning system

* The module `getchromsizes` was submitted to nf-core and moved from `local` to `nf-core`

* Added support for GFF files in IGV session generation

* [[#57](https://github.com/nf-core/cutandrun/issues/57), [#66](https://github.com/nf-core/cutandrun/issues/66)] - Upgraded version reporting in multiqc to support both software version by module and unique software versions. This improves detection of multi-version software usage in the pipeline

* [[#54](https://github.com/nf-core/cutandrun/issues/54)] - Fixed pipeline error where dots in sample ids inside the sample sheet were not correctly handled

* [[#75](https://github.com/nf-core/cutandrun/issues/75)] - Fixed error caused by emtpy peak files being passed to the `CALCULATE_FRIP` and `CALCULATE_PEAK_REPROD` python reporting modules

* [[#83]](https://github.com/nf-core/cutandrun/issues/83) - Fixed error in violin chart generation with cast to int64



### Software dependencies

bin/igv_files_to_session.py

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@@ -94,6 +94,10 @@ def igv_files_to_session(XMLOut,ListFile,Genome,PathPrefix=''): 
            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)

            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '

            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))

        elif extension in ['.gff']:

            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)

            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '

            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))

        elif extension in ['.bam']:

            pass

        else:

bin/lib/reports.py

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@@ -539,7 +539,7 @@ class Reports: 


        ## add peak width column

        self.seacr_beds['peak_width'] = self.seacr_beds['end'] - self.seacr_beds['start']

        self.seacr_beds['peak_width'] = self.seacr_beds['peak_width'].abs()

        self.seacr_beds['peak_width'] = self.seacr_beds['peak_width'].abs().astype('float64')



        ax = sns.violinplot(data=self.seacr_beds, x="group", y="peak_width", hue="replicate", palette = "viridis")

        ax.xaxis.set_tick_params(labelrotation=45)

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