Add pychopper instead porechop not functionnal

src/.docker_modules/pychopper/2.5.0/Dockerfile

+# SPDX-FileCopyrightText: 2023 Xavier Grand <xavier.grand@inserm.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM continuumio/miniconda3
+MAINTAINER Xavier Grand
+
+RUN apt-get update && apt-get install -y procps
+
+ENV PYCHOPPER_VERSION="2.5.0"
+RUN conda init \
+&& conda config --add channels r \
+&& conda config --add channels defaults \
+&& conda config --add channels conda-forge \
+&& conda config --add channels bioconda \
+&& conda create -y -n pychopper
+SHELL ["conda", "run", "-n", "pychopper", "/bin/bash", "-c"]
+RUN conda install -c nanoporetech -c conda-forge -c bioconda "nanoporetech::pychopper" \
+&& echo "conda activate pychopper" >> /root/.bashrc
+
+ENV PATH /usr/local/envs/pychopper/bin:/usr/local/condabin:$PATH
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src/.docker_modules/pychopper/2.5.0/docker_init.sh

+#!/bin/sh
+# docker pull lbmc/pychopper:2.5.0
+# docker build src/.docker_modules/pychopper/2.5.0 -t 'lbmc/pychopper:2.5.0'
+# docker push lbmc/pychopper:2.5.0
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/pychopper:2.5.0" --push src/.docker_modules/pychopper/2.5.0
+
+# docker pull xgrand/pychopper:2.5.0
+docker build src/.docker_modules/pychopper/2.5.0 -t 'xgrand/pychopper:2.5.0'
+docker push xgrand/pychopper:2.5.0
+# docker buildx build --platform linux/amd64,linux/arm64 -t "xgrand/pychopper:2.5.0" --push src/.docker_modules/pychopper/2.5.0
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src/bolero.nf

@@ -84,9 +84,9 @@ params.skipBC = true
 params.gpu_mode = false
 params.adapt = "CGACTGGAGCACGAGGACACTGA" // "CGACTGGAGCACGAGGACACTGACATGGACTGAAGGAGTAGAAA" //  
 params.gsp = "TTAGGCAGAGGTGAAAAAGTTG"
-params.transcriptome = "./data/202201_Full-length_HBV_GTFv3/20220112_preCore_FL_HBV_XGR_transcripts.fasta"
-params.genome = "./data/202201_Full-length_HBV_GTFv3/preCore_XGR.fasta"
-params.gtf = "./data/202201_Full-length_HBV_GTFv3/20220112_GTF_preCore_FL_HBV_XGR.gtf"
+// params.transcriptome = "./data/202201_Full-length_HBV_GTFv3/20220112_preCore_FL_HBV_XGR_transcripts.fasta"
+params.genome = "/home/xavier/Data/Genome/202201_Full-length_HBV_GTFv3/20230516_HBV_FL_preCore_reference.fasta"
+params.gtf = "/home/xavier/Data/Genome/202201_Full-length_HBV_GTFv3/20230516_GTF_preCore_FL_HBV_XGR.gtf"
 
 params.flowcell = "FLO-MIN106"
 params.kit = "SQK-PBK004"
@@ -188,7 +188,9 @@ include { start_position_individuals } from "./nf_modules/start_positions/main.n
 include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
 include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf"
 include { rna_count } from "./nf_modules/rna_count/main.nf"
+
 include { porechop } from "./nf_modules/porechop/main.nf"
+include { trimmming_pychopper } from "./nf_modules/pychopper/main.nf"
 
 /*
  ****************************************************************
@@ -250,9 +252,13 @@ workflow {
 
   //Trimming with porechop
   porechop(seqkit_grep.out.filtered_fastq)
+
+  //Trimming with pychopper
+  //trimmming_pychopper(seqkit_grep.out.filtered_fastq)
   
   //Cut of the 5'RACE sequence
   cut_5pRACE(porechop.out.porechoped_fastq, params.adapt)
+  //cut_5pRACE(trimmming_pychopper.out.pychoped_fastq, params.adapt)
   //cut_5pRACE(seqkit_grep.out.filtered_fastq, params.adapt)
 
   //########################## MAPPING ##########################
@@ -304,3 +310,22 @@ workflow {
   rna_count(files_for_rna_count)
 
 }
+
+// End message:
+
+workflow.onComplete {
+
+   println ( workflow.success ? """
+       DUPFinder tools execution summary
+       ---------------------------
+       Completed at	: ${workflow.complete}
+       Duration    	: ${workflow.duration}
+       Success     	: ${workflow.success}
+       workDir     	: ${workflow.workDir}
+       exit status 	: ${workflow.exitStatus}
+       """ : """
+       Failed: ${workflow.errorReport}
+       exit status : ${workflow.exitStatus}
+       """
+   )
+}

src/nf_modules/pychopper/main.nf

+version = "2.5.0"
+container_url = "xgrand/pychopper:${version}"
+
+params.pychopper_out =""
+process trimmming_pychopper {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${barcode}"
+  if (params.pychopper_out != "") {
+    publishDir "results/${params.pychopper_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(barcode), path(fastq)
+
+  output:
+    tuple val(barcode), path("${barcode}/${barcode}_merged_pychoped.fastq.gz"), emit: pychoped_fastq
+
+  script:
+"""
+mkdir ${barcode}
+cd ${barcode}/
+pychopper -k ${params.kit} -r ${barcode}_pychopper_report.pdf -S ${barcode}_statistics.tsv -t ${task.cpus} ../${fastq} ${barcode}_merged_pychoped.fastq.gz
+"""
+}
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