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added fc_count_type parameter to biotype_qc command #441

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merged 2 commits into from
Aug 17, 2020
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added fc_count_type parameter to biotype_qc command #441

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26d9352
added fc_count_type parameter to biotype_qc command
pcantalupo Jul 14, 2020
14d847a
Update CHANGELOG.md
pcantalupo Jul 14, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@
* Fixes broken links [#357](https://github.com/nf-core/rnaseq/issues/357)
* Fixes label name in FastQC process [#345](https://github.com/nf-core/rnaseq/pull/345)
* Make publishDir mode configurable [#391](https://github.com/nf-core/rnaseq/pull/391)
* Fixed issue where featureCounts process fails when setting --fc_count_type to gene [#440](https://github.com/nf-core/rnaseq/issues/440)
* Add AWS tests GitHub actions workflow for small tests
* Optimise MultiQC configuration for faster run-time on huge sample numbers
* Build Docker image using GitHub Actions
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -1564,7 +1564,7 @@ if (!params.skipAlignment) {
}
// Try to get real sample name
sample_name = bam_featurecounts.baseName - 'Aligned.sortedByCoord.out' - '_subsamp.sorted'
biotype_qc = params.skipBiotypeQC ? '' : "featureCounts -a $gtf -g $biotype -o ${bam_featurecounts.baseName}_biotype.featureCounts.txt -p -s $featureCounts_direction $bam_featurecounts"
biotype_qc = params.skipBiotypeQC ? '' : "featureCounts -a $gtf -g $biotype -t ${params.fc_count_type} -o ${bam_featurecounts.baseName}_biotype.featureCounts.txt -p -s $featureCounts_direction $bam_featurecounts"
mod_biotype = params.skipBiotypeQC ? '' : "cut -f 1,7 ${bam_featurecounts.baseName}_biotype.featureCounts.txt | tail -n +3 | cat $biotypes_header - >> ${bam_featurecounts.baseName}_biotype_counts_mqc.txt && mqc_features_stat.py ${bam_featurecounts.baseName}_biotype_counts_mqc.txt -s $sample_name -f rRNA -o ${bam_featurecounts.baseName}_biotype_counts_gs_mqc.tsv"
"""
featureCounts -a $gtf -g ${params.fc_group_features} -t ${params.fc_count_type} -o ${bam_featurecounts.baseName}_gene.featureCounts.txt $extraAttributes -p -s $featureCounts_direction $bam_featurecounts
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