new version

Author: lucacozzuto

.github/workflows/build.yml

@@ -52,4 +52,4 @@ jobs:
 
         env:
           NXF_ANSI_LOG: false
-          NXF_VER: 24.04.4
+          NXF_VER: 25.04.5

README.md

@@ -1,7 +1,7 @@
 # MoP4 - Master of Pores 4
 [![Docker Build Status](https://img.shields.io/docker/automated/biocorecrg/nanopore.svg)](https://cloud.docker.com/u/biocorecrg/repository/docker/biocorecrg/nanopore/builds)
 [![mop4-CI](https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml/badge.svg)](https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Nextflow version](https://img.shields.io/badge/Nextflow-24.04.4-brightgreen)](https://www.nextflow.io/)
+[![Nextflow version](https://img.shields.io/badge/Nextflow-25.04.5-brightgreen)](https://www.nextflow.io/)
 [![Nextflow DSL2](https://img.shields.io/badge/Nextflow-DSL2-brightgreen)](https://www.nextflow.io/)
 [![Singularity version](https://img.shields.io/badge/Singularity-v3.2.1-green.svg)](https://www.sylabs.io/)
 [![Docker version](https://img.shields.io/badge/Docker-v20.10.8-blue)](https://www.docker.com/)

conf/m1_apple.config

@@ -1,3 +1,7 @@
+docker {
+    enabled = true
+}
+
 process {
     executor = 'local'
     cpus = 1

docs/changelog.rst

@@ -7,6 +7,15 @@ CHANGELOG
 .. autosummary::
    :toctree: generated
 
+Version 4.1
+================
+
+* mop_preprocess
+   * Updated Nextflow version to 25.04.5.
+   * Added a stats file (MultiQC standard) with total number of reads, accepted reads, and percentages.
+   * Added Python container support for ADAPTIVE_SAMPLINGQC.
+   * Added support for tRNA demultiplexing with seqtagger-trna.
+
 Version 4.0
 ================
 Removed mop_tail and added mop_dna and mop_utils

docs/tutorial.rst

@@ -176,7 +176,7 @@ You will get this as output.
    ⢰⣿⣿⠀⠈⢉⡶⢿⣿⣿⣿⣿⣿⣿⣿⣿⣆⠀⠙⢇⠈⢿⣶⣦⣤⣀⣀⣠⣤⣶⣿⣿⡿⠛⠁⢀⣤⣾⣿⣿⡿⠁⠀⠀⠀⠀⠀⠀⠀⣸⣿⡿⠿⠋⠙⠒⠄⠀⠉⡄
    ⣿⣿⡏⠀⠀⠁⠀⠀⠀⠉⠉⠙⢻⣿⣿⣿⣿⣷⡀⠀⠀⠀⠻⣿⣿⣿⣿⣿⠿⠿⠛⠁⠀⣀⣴⣿⣿⣿⣿⠟⠀⠀⠀⠀⠀⠀⠀⠀⢠⠏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠰
    ====================================================
-   BIOCORE@CRG Master of Pores 4. Preprocessing - N F  ~  version 4.0
+   BIOCORE@CRG Master of Pores 4. Preprocessing - N F  ~  version 4.1
    ====================================================
    
    
@@ -334,7 +334,7 @@ You can run the pipeline on Linux in local using docker or singularity as a cont
    ⢰⣿⣿⠀⠈⢉⡶⢿⣿⣿⣿⣿⣿⣿⣿⣿⣆⠀⠙⢇⠈⢿⣶⣦⣤⣀⣀⣠⣤⣶⣿⣿⡿⠛⠁⢀⣤⣾⣿⣿⡿⠁⠀⠀⠀⠀⠀⠀⠀⣸⣿⡿⠿⠋⠙⠒⠄⠀⠉⡄
    ⣿⣿⡏⠀⠀⠁⠀⠀⠀⠉⠉⠙⢻⣿⣿⣿⣿⣷⡀⠀⠀⠀⠻⣿⣿⣿⣿⣿⠿⠿⠛⠁⠀⣀⣴⣿⣿⣿⣿⠟⠀⠀⠀⠀⠀⠀⠀⠀⢠⠏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠰
    ====================================================
-   BIOCORE@CRG Master of Pores 4. Preprocessing - N F  ~  version 4.0
+   BIOCORE@CRG Master of Pores 4. Preprocessing - N F  ~  version 4.1
    ====================================================
    
    

launch_nf.sh

@@ -15,6 +15,7 @@ _term() {
 
 trap _term TERM
 
+export NXF_VER="25.04.5"
 export NXF_JVM_ARGS="-Xms2g -Xmx6g"
 
 "$@" & pid=$!

mop_preprocess/launch_nf.sh

@@ -10,7 +10,7 @@ nextflow.enable.dsl=2
  */
 
 // Pipeline version
-version = '4.0'
+version = '4.1'
 
 params.help            = false
 params.resume          = false
@@ -157,6 +157,9 @@ switch(params.demultiplexing) {
     case "seqtagger":
         demux_models = "${projectDir}/seqtagger_models/"
     break;
+    case "seqtagger-trna":
+        demux_models = "${projectDir}/seqtagger_tRNA_models/"
+    break;
     case "dorado":
         demux_models = "${projectDir}/seqtagger_models/"
     break;
@@ -228,12 +231,16 @@ checkTools(tools, params.progPars)
 progPars["basecalling"]["dorado-mod"] = progPars["basecalling"]["dorado-mod"] + " --emit-moves"
 
 def basecaller_pars = ["dorado" : progPars["basecalling"]["dorado"],  "dorado-duplex" : progPars["basecalling"]["dorado"], "dorado-mod" : progPars["basecalling"]["dorado-mod"] ]
-def demux_pars = [ "dorado" : progPars["basecalling"]["dorado"] + " " + progPars["demultiplexing"]["dorado"], "seqtagger":  progPars["demultiplexing"]["seqtagger"] ]
+def demux_pars = [ "dorado" : progPars["basecalling"]["dorado"] + " " + progPars["demultiplexing"]["dorado"], "seqtagger":  progPars["demultiplexing"]["seqtagger"], "seqtagger-trna":  progPars["demultiplexing"]["seqtagger-trna"] ]
 def mapping_pars = ["bwa": progPars["mapping"]["bwa"], "winnowmap": progPars["mapping"]["winnowmap"] + " -y",
 				"graphmap2": progPars["mapping"]["graphmap2"], "minimap2": progPars["mapping"]["minimap2"] + " -y --MD",
 				"graphmap": progPars["mapping"]["graphmap"]
 				]
 
+if (params.demultiplexing == "seqtagger-trna") {
+	dem_cont = "lpryszcz/seqtagger:1.1a"
+}
+
 // INCLUDE WORKFLOWS
 include { BASECALL } from "${workflowsDir}/basecaller" addParams(gpu: gpu_bc, output: output_bc, label: basecall_label, label2:'big_cpus', type:basecalling ,  extrapars: basecaller_pars[basecalling], models: dorado_models )
 include { DEMULTIPLEX } from "${workflowsDir}/demultiplexer.nf" addParams(gpu: gpu, output: output_bc, label: basecall_label, type:params.demultiplexing , extrapars: demux_pars[params.demultiplexing], models: demux_models )
@@ -467,6 +474,7 @@ workflow {
 
             switch(params.demultiplexing) {
                 case "seqtagger":
+                case "seqtagger-trna":
                 	outbc = BASECALL(pod5_4_analysis)
                 	demux = DEMULTIPLEX(pod5_4_analysis, outbc.basecalled_fastq)
                 	demufq = demux.demultiplexed_fastq

mop_preprocess/mop_preprocess.nf

@@ -8,7 +8,7 @@ GPU: "cuda11"
 basecalling: "dorado"
 #For emitting the move tables (with dorado-mod)
 emit_moves: ""
-## Demultiplexing can be either dorado (for DNA) / seqtagger (for RNA)
+## Demultiplexing can be either dorado (for DNA) / seqtagger (for RNA) / seqtagger-trna (for tRNA)
 demultiplexing: "dorado"
 ### For demultiplexing pod5 files
 demulti_pod5: "NO"
@@ -50,6 +50,7 @@ progPars:
     dorado-duplex: "sup"
   demultiplexing:
     seqtagger: "-k b100"
+    seqtagger-trna: "-k b07_RNA004_tRNA"
     dorado: "--sequencing-kit EXP-NBD104 --no-trim"
   filtering:
     nanofilt: ""

mop_preprocess/params.dem.yaml

@@ -6,7 +6,7 @@ pod5: "${projectDir}/../data/dMOD/**/*.pod5"
 GPU: "cuda11"
 # Basecalling can be either NO, dorado, dorado-mod or dorado-duplex
 basecalling: "dorado-mod"
-## Demultiplexing can be either dorado (for DNA) / seqtagger (for RNA)
+## Demultiplexing can be either dorado (for DNA) / seqtagger (for RNA) / seqtagger-trna (for tRNA)
 #demultiplexing: "seqtagger"
 demultiplexing: "NO"
 demulti_pod5: "NO"
@@ -48,6 +48,7 @@ progPars:
     dorado-duplex: "sup"
   demultiplexing:
     seqtagger: "-k b100"
+    seqtagger-trna: "-k b07_RNA004_tRNA"
     dorado: ""
   filtering:
     nanofilt: ""