From f2dca0931db5b0046d0407a0bda4618ffbc987be Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Thu, 1 Jun 2023 16:42:16 +0200
Subject: [PATCH] =?UTF-8?q?Ajout=20de=20l'outil=20ps=20au=20dockerfile=20r?=
=?UTF-8?q?-bolero=20et=20r=C3=A9solution=20d'erreurs=20dans=20la=20foncti?=
=?UTF-8?q?on=20concatenate=20de=20seqkit?=
MIME-Version: 1.0
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---
src/.docker_modules/r-bolero/1.0/Dockerfile | 7 ++++++-
src/bolero.nf | 17 ++++++++---------
src/nf_modules/seqkit/main.nf | 5 +++--
3 files changed, 17 insertions(+), 12 deletions(-)
diff --git a/src/.docker_modules/r-bolero/1.0/Dockerfile b/src/.docker_modules/r-bolero/1.0/Dockerfile
index 3407ad5..de41dda 100644
--- a/src/.docker_modules/r-bolero/1.0/Dockerfile
+++ b/src/.docker_modules/r-bolero/1.0/Dockerfile
@@ -3,9 +3,14 @@ LABEL AUTHOR="Alia Rifki"
LABEL MAINTAINER="Xavier Grand <xavier.grand@inserm.fr>"
LABEL build_date="2023-05-26"
-## copy Rscript files
+## Copy all Rscript files
COPY ./*.R .
+## Install packages
RUN Rscript Install_packages.R
+RUN apt-get update && apt-get install -y procps
+
+## Langage
CMD ["bash"]
+
diff --git a/src/bolero.nf b/src/bolero.nf
index 41e7bda..3ff3c53 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -53,7 +53,7 @@ def helpMessage() {
--chunk_size [int] Chunck size, default = 1900 (refer to guppy manual).
Help:
- --help Display this help message.
+ --help | --h Display this help message.
""".stripIndent()
}
@@ -111,7 +111,6 @@ params.pycoQC_out = "pycoQC/"
****************************************************************
*/
-//to print multiline informations
log.info "fast5/q folder : ${params.input}"
log.info "5'RACE adapter sequence : ${params.adapt}"
if(!params.skipBC) log.info "Guppy basecalling calculation using GPU mode : ${params.gpu_mode}."
@@ -163,8 +162,9 @@ if(!params.skipBC) {
}
// Replace concatenate by seqkit fct to parallelization:
-// include { concatenate } from "./nf_modules/seqkit/main.nf"
-include { concatenate } from "./nf_modules/concatenate/main.nf"
+include { concatenate } from "./nf_modules/seqkit/main.nf"
+//include { concatenate } from "./nf_modules/concatenate/main.nf"
+
include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
include { hbv_genome } from "./nf_modules/minimap2/main.nf"
include { seqkit_grep } from "./nf_modules/seqkit/main.nf"
@@ -177,9 +177,6 @@ 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"
-/////////////////////////////////////////////////////////
-// script R avec classification des reads par type d'ARN et graphiques associés
-
// creation des fonctions NanoSplicer:
// include { jwr_check } from "./nf_modules/nanosplicer/main.nf"
@@ -211,7 +208,7 @@ workflow {
}
}
//####################### PREPROCESSING #######################
-
+
//Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
@@ -220,8 +217,10 @@ workflow {
//Cut of the 5'RACE sequence
cut_5pRACE(seqkit_grep.out.filtered_fastq, params.adapt)
- //########################## MAPPING ##########################
+
+ //########################## MAPPING ##########################
+
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome)
sort_index_bam(hbv_genome.out.bam)
diff --git a/src/nf_modules/seqkit/main.nf b/src/nf_modules/seqkit/main.nf
index 3f2cb3b..e6d7e6b 100755
--- a/src/nf_modules/seqkit/main.nf
+++ b/src/nf_modules/seqkit/main.nf
@@ -71,14 +71,15 @@ process concatenate {
}
input:
- path(fastq_dir)
+ path fastq
output:
path "merged.fastq.gz", emit: merged_fastq
script:
"""
- seqkit scat -j ${tasks.cpus} -f ${fastq_dir} --gz-only > merged.fastq
+ path=\$(readlink -f ${fastq})
+ seqkit scat -j ${task.cpus} -f \${path} --gz-only > merged.fastq
gzip merged.fastq
"""
}
\ No newline at end of file
--
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