add bed file for mosdepth

nf-core · Oct 18, 2023 · dd78863 · dd78863
1 parent 0f94b46
commit dd78863
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Showing 4 changed files with 5 additions and 8 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -178,11 +178,6 @@ process {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
     }
 
-    withName: REFORMAT {
-        ext.args = "forcetrimright=75"
-        ext.args2 = "forcetrimleft=75"
-    }
-
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf
@@ -18,7 +18,7 @@ workflow FUSIONINSPECTOR_WORKFLOW {
         ch_versions = Channel.empty()
         index ="${params.starfusion_ref}"
 
-        ch_fusion_list = ( params.fusioninspector_filter ? fusion_list_filtered : fusion_list )
+        ch_fusion_list = ( params.tools_cutoff > 1 ? fusion_list_filtered : fusion_list )
         .branch{
             no_fusions: it[1].size() == 0
             fusions: it[1].size() > 0

diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf
@@ -15,11 +15,12 @@ workflow QC_WORKFLOW {
         ch_fasta
         ch_fai
         ch_rrna_interval
+        ch_rrna_intervals_bed
 
     main:
         ch_versions = Channel.empty()
 
-        MOSDEPTH(ch_bam_sorted_indexed.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), ch_fasta)
+        MOSDEPTH(ch_bam_sorted_indexed.combine(ch_rrna_intervals_bed.map{ meta, bed -> [ bed?:[] ] }), ch_fasta)
         ch_versions = ch_versions.mix(MOSDEPTH.out.versions)
         ch_mosdepth_summary = Channel.empty().mix(MOSDEPTH.out.summary_txt)
         ch_mosdepth_global = Channel.empty().mix(MOSDEPTH.out.global_txt)

diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
@@ -264,7 +264,8 @@ workflow RNAFUSION {
         ch_refflat,
         ch_fasta,
         ch_fai,
-        ch_rrna_interval
+        ch_rrna_interval,
+        ch_rrna_interval_bed
     )
     ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions.first().ifEmpty(null))