Fix some common problems in CIRIquant and HISAT2_ALIGN

nf-core · Mar 18, 2024 · 72dd514 · 72dd514
1 parent c4a3e8e
commit 72dd514
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf
@@ -7,8 +7,8 @@ process CIRIQUANT_YML {
         'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }"
 
     input:
-    path gtf
-    path fasta
+    tuple val(meta), path(gtf)
+    tuple val(meta2), path(fasta)
     path bwa
     path hisat2
 
@@ -19,7 +19,7 @@ process CIRIQUANT_YML {
     task.ext.when == null || task.ext.when
 
     script:
-    hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/
+    hisat2_prefix = meta2.id
     fasta_path = fasta.toRealPath()
     gtf_path = gtf.toRealPath()
     bwa_path = bwa.toRealPath()

diff --git a/nextflow.config b/nextflow.config
@@ -206,6 +206,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.runOptions   = '--no-mount tmp --writable-tmpfs'
     }
     gitpod {
         executor.name          = 'local'

diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf
@@ -141,7 +141,7 @@ workflow CIRCRNA_DISCOVERY {
 
     // only need path to bwa, only need path to hisat2.
     // do not want to upset the collect declr for all indices just for this.
-    CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } )
+    CIRIQUANT_YML( ch_gtf, ch_fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } )
     CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() )
     CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads )