TEST remove count process

workflow/rna-seq.nf

@@ -404,25 +404,3 @@ process makeBigWig {
     """
 }
 
-/*
- *Run featureCounts and get the counts, tpm, and fpkm
-*/
-process makeFeatureCounts {
-  tag "${repRID}"
-  publishDir "${outDir}/featureCounts", mode: 'copy', pattern: "${repRID}*.featureCounts*"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.makeFetureCounts.{out,err}"
-
-  input:
-    path script_calculateTPM
-    tuple val (repRID1), path (bam), path (bai) from featureCountsIn
-    tuple val (repRID2), path (genome), path (gtf) from featureCountsRef
-
-  output:
-    tuple val ("${repRID}"), path ("${repRID}.featureCounts.summary"), path ("${repRID}.featureCounts"), path ("${bam}.featureCounts.sam") into featureCountsOut
-
-  script:
-    """
-    featureCounts -R SAM -p -G ${genome} -T `nproc` -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam
-    Rscript calculateTPM.R --count "${repRID}.featureCounts"
-    """
-}