Merge pull request #113 from nf-core/ciriquant-yml

Remove problematic ciriquant-yml process
nf-core · Apr 20, 2024 · c29124f · c29124f
2 parents 3e742a9 + e14ceae
commit c29124f
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Showing 3 changed files with 19 additions and 45 deletions.
diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf
@@ -9,7 +9,10 @@ process CIRIQUANT {
 
     input:
     tuple val(meta), path(reads)
-    path yml
+    tuple val(meta2), path(gtf)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(bwa)
+    tuple val(meta5), path(hisat2)
 
     output:
     tuple val(meta), path("${prefix}/${prefix}.gtf"), emit: gtf
@@ -24,11 +27,24 @@ process CIRIQUANT {
     prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.1.0'
     """
+    BWA=`which bwa`
+    HISAT2=`which hisat2`
+    STRINGTIE=`which stringtie`
+    SAMTOOLS=`which samtools`
+
+    BWA_FILE=`ls ${bwa}/*.bwt`
+    BWA_PREFIX=`basename \$BWA_FILE .bwt`
+
+    HISAT2_FILE=`ls ${hisat2}/*.1.ht2`
+    HISAT2_PREFIX=`basename \$HISAT2_FILE .1.ht2`
+
+    printf "name: ciriquant\\ntools:\\n  bwa: \$BWA\\n  hisat2: \$HISAT2\\n  stringtie: \$STRINGTIE\\n  samtools: \$SAMTOOLS\\n\\nreference:\\n  fasta: ${fasta}\\n  gtf: ${gtf}\\n  bwa_index: ${bwa}/\$BWA_PREFIX\\n  hisat_index: ${hisat2}/\$HISAT2_PREFIX" > config.yml
+
     CIRIquant \\
         -t ${task.cpus} \\
         -1 ${reads[0]} \\
         -2 ${reads[1]} \\
-        --config $yml \\
+        --config config.yml \\
         --no-gene \\
         -o ${prefix} \\
         -p ${prefix}

diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf
diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf
@@ -7,7 +7,6 @@ include { SAMTOOLS_INDEX                                 } from '../../modules/n
 include { FIND_CIRC_ANCHORS                              } from '../../modules/local/find_circ/anchors/main'
 include { FIND_CIRC                                      } from '../../modules/local/find_circ/find_circ/main'
 include { FIND_CIRC_FILTER                               } from '../../modules/local/find_circ/filter/main'
-include { CIRIQUANT_YML                                  } from '../../modules/local/ciriquant/yml/main'
 include { CIRIQUANT                                      } from '../../modules/local/ciriquant/ciriquant/main'
 include { CIRIQUANT_FILTER                               } from '../../modules/local/ciriquant/filter/main'
 include { CIRCRNA_FINDER_FILTER                          } from '../../modules/local/circrna_finder/filter/main'
@@ -141,8 +140,7 @@ 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( 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( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index )
     CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads )
 
     ch_versions = ch_versions.mix(CIRIQUANT.out.versions)