Cleanup for #143. Made featurecounts biotype work.

Author: ewels

CHANGELOG.md

@@ -11,6 +11,8 @@ Many thanks to everyone who gave us feedback about the pipeline!
     * **UPPMAX users now need to specify `--reverse_stranded` for the same behaviour**
 * Switched UPPMAX configuration to use Singularity instead of environment modules
 * Switched c3se Hebbe configuration to use Singularity & refactored config
+* Made output from DupRadar, Biotype Counts and edgeR sample similarity use [MultiQC Custom Content](http://multiqc.info/docs/#custom-content) formatting
+    * These results now show up in MultiQC reports for everyone, not just people with our [custom MultiQC plugin](https://github.com/ewels/MultiQC_NGI)
 * Added a Troubleshooting section to the docs
 * Fixed bug where BED12 generation failed when only GTF supplied.
 

assets/biotypes_header.txt

@@ -1,11 +1,11 @@
 #id: 'biotype-counts'
-#section_name: 'Biotypes'
-#section_href: 'http://bioinf.wehi.edu.au/featureCounts'
-#description: "shows reads overlapping genomic features of different biotypes."
+#section_name: 'Biotype Counts'
+#description: "shows reads overlapping genomic features of different biotypes,
+#    counted by <a href='http://bioinf.wehi.edu.au/featureCounts'>featureCounts</a>."
 #plot_type: 'bargraph'
+#anchor: 'featurecounts_biotype'
 #pconfig:
-#    title: featureCounts: 'Biotypes'
-#    xLog: True
-#    xlab: "expression (reads/kbp)"
-#    max: 100
-#    min: 0
+#    id: "featureCounts_biotype_plot"
+#    title: "featureCounts: Biotypes"
+#    xlab: "# Reads"
+#    cpswitch_counts_label: "Number of Reads"

conf/multiqc_config.yaml

@@ -1,6 +1,7 @@
 extra_fn_clean_exts:
     - _R1
     - _R2
+    - .hisat
 report_comment: >
     This report has been generated by the <a href="https://github.com/SciLifeLab/NGI-RNAseq" target="_blank">NGI-RNAseq</a>
     analysis pipeline. For information about how to interpret these results, please see the

main.nf

@@ -893,7 +893,7 @@ process featureCounts {
     tag "${bam_featurecounts.baseName - '.sorted'}"
     publishDir "${params.outdir}/featureCounts", mode: 'copy',
         saveAs: {filename ->
-            if (filename.indexOf("_biotype_counts.txt") > 0) "biotype_counts/$filename"
+            if (filename.indexOf("_biotype_counts_mqc.txt") > 0) "biotype_counts/$filename"
             else if (filename.indexOf("_gene.featureCounts.txt.summary") > 0) "gene_count_summaries/$filename"
             else if (filename.indexOf("_gene.featureCounts.txt") > 0) "gene_counts/$filename"
             else "$filename"
@@ -907,7 +907,7 @@ process featureCounts {
     output:
     file "${bam_featurecounts.baseName}_gene.featureCounts.txt" into geneCounts, featureCounts_to_merge
     file "${bam_featurecounts.baseName}_gene.featureCounts.txt.summary" into featureCounts_logs
-    file "${bam_featurecounts.baseName}_biotype_counts.txt" into featureCounts_biotype
+    file "${bam_featurecounts.baseName}_biotype_counts_mqc.txt" into featureCounts_biotype
     file '.command.log' into featurecounts_stdout
 
     script:
@@ -920,8 +920,8 @@ process featureCounts {
     """
     featureCounts -a $gtf -g gene_id -o ${bam_featurecounts.baseName}_gene.featureCounts.txt -p -s $featureCounts_direction $bam_featurecounts
     featureCounts -a $gtf -g gene_biotype -o ${bam_featurecounts.baseName}_biotype.featureCounts.txt -p -s $featureCounts_direction $bam_featurecounts
-    cut -f 1,7 ${bam_featurecounts.baseName}_biotype.featureCounts.txt | tail -n 7 > tmp_file 
-    cat $biotypes_header tmp_file >> ${bam_featurecounts.baseName}_biotype_counts.txt
+    cut -f 1,7 ${bam_featurecounts.baseName}_biotype.featureCounts.txt | tail -n 7 > tmp_file
+    cat $biotypes_header tmp_file >> ${bam_featurecounts.baseName}_biotype_counts_mqc.txt
     """
 }
 
@@ -1015,7 +1015,7 @@ process sample_correlation {
     """
     edgeR_heatmap_MDS.r "rlocation=$rlocation" $input_files
     cat $mdsplot_header edgeR_MDS_Aplot_coordinates_mqc.csv >> tmp_file
-    mv tmp_file edgeR_MDS_Aplot_coordinates_mqc.csv 
+    mv tmp_file edgeR_MDS_Aplot_coordinates_mqc.csv
     cat $heatmap_header log2CPM_sample_distances_mqc.csv >> tmp_file
     mv tmp_file log2CPM_sample_distances_mqc.csv
     """