Remove spices process and merged output

data/md5s.txt

@@ -77,7 +77,5 @@ cbc2c821e5c1cea84771446f1e48c57e *data/all.A.exc.tsv
 d079a559fc31561e625d8a6032e97e66 *data/all.A.psi5.tsv
 4569c6d8eaf78d750df5c7b2cc62b1fe *data/all.A.psit.tsv
 3a4b9a7bf23c0806a2f024157123839e *data/all.A.ret.tsv
-bd86b7e5a22bb838605e9ada3fb1ee7a *data/all.B.psicas.tsv
-bd86b7e5a22bb838605e9ada3fb1ee7a *data/all.B.psiloc.tsv
 2e3f45e2b7a9d5d3ca4378a2b2f5fd26 *data/all.counts.ssc.tsv
 1d6fa775fbf99767f84e4bd982601a63 *data/all.counts.ssj.tsv

ipsa.nf

@@ -487,25 +487,6 @@ process zeta {
   """
 }
 
-process psicas {
-
-  publishDir "${params.dir}/${endpoint}"
-
-  input:
-  file annotation from txIdxPsicas
-  set id, file(ssj) from ssj4psicasA06
-
-  output:
-  set id, file("${prefix}.gff") into B07
-
-  script:
-  endpoint = 'B07'
-  prefix = ssj.name.replace(/.tsv/,'').replace(/A06.ssj/, endpoint)
-  """
-  psicas.pl -ssj ${ssj} -annot ${annotation} -mincount ${params.mincount} > ${prefix}.gff 
-  """
-}
-
 process zetaMex {
 
   publishDir "${params.dir}/${endpoint}"
@@ -543,14 +524,6 @@ if ( params.microexons ) {
     }.set { A074merge }
 }
 
-B07.toSortedList { a,b -> a[0] <=> b[0] }
-  .map { list ->
-    ids = []
-    gffs = []
-    list.each { ids << it[0]; gffs << it[1] }
-    [ids, gffs]
-  }.set { B074merge }
-
 process mergeGFFzeta {
   publishDir "${params.dir}"
 
@@ -580,26 +553,6 @@ process mergeGFFzeta {
   template 'merge_gff.pl'
 }
 
-process mergeGFFpsicas {
-  publishDir "${params.dir}"
-
-  input:
-  set ids, file(sscs) from B074merge
-
-  output:
-  file "${prefix}.psicas.tsv"
-  file "${prefix}.psiloc.tsv"
-
-  shell:
-  prefix = "${params.merge}.B"
-  input = [sscs.toList(), ids].transpose().flatten().collect { "'$it'" }.join(',')
-  features = ['psicas', 'psiloc']
-  output = features.collect { "'${it}', '${prefix}.${it}.tsv'" }.join(',')
-  percent = 0.25
-  transf = 'log'
-  template 'merge_gff.pl'
-}
-
 process ssjTsv2bed {
 
   publishDir "${params.dir}/${endpoint}"