add kmermerclust_clust process and switch to v0.1.0 of kmerclust

src/bin/kmerclust_boot.R

 library(kmerclust)
+library(tidyverse)
 args <- commandArgs(trailingOnly = TRUE)
 print(args)
 load(file = paste0(args[1], ".Rdata"))
 res <- count %>%
   dplyr::select(count_m, count_f) %>%
+  mutate(
+    count_m = round(count_m),
+    count_f = round(count_f)
+  ) %>%
+  dplyr::filter(count_m + count_f > 0) %>%
   as.matrix() %>%
-  poiss_compare_models(count, nboot = as.numeric(args[2]) * 2, frac = 1e-3, bootsize = 1, core = as.numeric(args[2]))
+  poiss_compare_models(count, nboot = as.numeric(args[2]) * 2, nbatch = 100, max_iter = 1e4, bootsize = 1, core = as.numeric(args[2]))
 save(res, file = paste0(args[1], "_boot_", args[3], ".Rdata"))
 
-

src/main.nf

@@ -35,6 +35,7 @@ workflow {
   COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
   KMERCLUST_LOAD(COLLATEKMER.out.csv, params_csv.collect())
   KMERCLUST_BOOT(Channel.of(1..params.bootstrap).combine(KMERCLUST_LOAD.out.rdata))
+  KMERCLUST_CLUST(Channel.of(["XY", "XO", "OO"]).combine(KMERCLUST_LOAD.out.rdata))
   KMERCLUST_MERGE(KMERCLUST_BOOT.out.rdata.groupTuple())
   KMERCLUST_PLOT(KMERCLUST_MERGE.out.rdata.mix(KMERCLUST_LOAD.out.rdata).groupTuple())
 }

src/modules/kmerclust.nf

@@ -2,7 +2,7 @@ process KMERCLUST_LOAD {
     tag "$specie"
     label 'big_mem_mono_cpus'
 
-    container "lbmc/kmerclust:0.0.7"
+    container "lbmc/kmerclust:0.1.0"
     publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
 
     input:
@@ -20,7 +20,7 @@ process KMERCLUST_LOAD {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rkmerclust: 0.0.7 
+        Rkmerclust: 0.1.0 
     END_VERSIONS
     """
 }
@@ -29,7 +29,7 @@ process KMERCLUST_BOOT {
     tag "$specie"
     label 'big_mem_multi_cpus'
 
-    container "lbmc/kmerclust:0.0.7"
+    container "lbmc/kmerclust:0.1.0"
     publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
 
     input:
@@ -46,16 +46,16 @@ process KMERCLUST_BOOT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rkmerclust: 0.0.7 
+        Rkmerclust: 0.1.0 
     END_VERSIONS
     """
 }
 
-process KMERCLUST {
+process KMERCLUST_CLUST {
     tag "$specie"
-    label 'big_mem_multi_cpus'
+    label 'small_mem_mono_cpus'
 
-    container "lbmc/kmerclust:0.0.7"
+    container "lbmc/kmerclust:0.1.0"
     publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
 
     input:
@@ -68,11 +68,11 @@ process KMERCLUST {
     script:
     def args = task.ext.args ?: ''
     """
-    Rscript ${projectDir}/bin/kmerclust.R ${specie} ${task.cpus}
+    Rscript ${projectDir}/bin/kmerclust_clust.R ${specie} ${task.cpus} ${id}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rkmerclust: 0.0.7 
+        Rkmerclust: 0.1.0 
     END_VERSIONS
     """
 }
@@ -81,7 +81,7 @@ process KMERCLUST_MERGE {
     tag "$specie"
     label 'big_mem_mono_cpus'
 
-    container "lbmc/kmerclust:0.0.7"
+    container "lbmc/kmerclust:0.1.0"
     publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
 
     input:
@@ -98,7 +98,7 @@ process KMERCLUST_MERGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rkmerclust: 0.0.7 
+        Rkmerclust: 0.1.0 
     END_VERSIONS
     """
 }
@@ -107,7 +107,7 @@ process KMERCLUST_PLOT {
     tag "$specie"
     label 'big_mem_mono_cpus'
 
-    container "lbmc/kmerclust:0.0.7"
+    container "lbmc/kmerclust:0.1.0"
     publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
 
     input:
@@ -124,7 +124,7 @@ process KMERCLUST_PLOT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rkmerclust: 0.0.7 
+        Rkmerclust: 0.1.0 
     END_VERSIONS
     """
 }