From 3b7be876be77f9d54bd6d454ca6e3d1001ed1ea0 Mon Sep 17 00:00:00 2001 From: elabaron <emmanuel.labaronne@ens-lyon.fr> Date: Tue, 20 Oct 2020 22:11:56 +0200 Subject: [PATCH] add coverage option in pipeline --- src/RNAseq.config | 19 ++++++++++++++----- src/RNAseq.nf | 24 +++++++++++++++++++++++- src/RibosomeProfiling.nf | 22 +++++++++++++++++++++- 3 files changed, 58 insertions(+), 7 deletions(-) diff --git a/src/RNAseq.config b/src/RNAseq.config index 877109ba..a6909dd4 100644 --- a/src/RNAseq.config +++ b/src/RNAseq.config @@ -57,10 +57,19 @@ profiles { clusterOptions = "-cwd -V" memory = "20GB" cpus = 16 - penv = 'openmp16' + penv = 'openmp16' + time = "12h" + queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' + } + withName: coverage { + container = "lbmc/deeptools:3.0.2" + executor = "sge" + clusterOptions = "-cwd -V" + memory = "20GB" + cpus = 16 + penv = 'openmp16' time = "12h" queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' - penv = 'openmp16' } withName: fastqc_genome { container = "lbmc/fastqc:0.11.5" @@ -119,7 +128,7 @@ profiles { queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' } withName: rnaseq_qc { - container = "gcr.io/broad-cga-aarong-gtex/rnaseqc:2.3.6" + module = "RNAseq-QC/2.3.6" executor = "sge" clusterOptions = "-cwd -V" cpus = 1 @@ -193,8 +202,8 @@ profiles { container = "lbmc/multiqc:1.7" cpus = 1 } - withName: coverage_genome { - container = "lbmc/deeptools:3.1.1" + withName: coverage { + container = "lbmc/deeptools:3.0.2" cpus = 8 } } diff --git a/src/RNAseq.nf b/src/RNAseq.nf index ebe2ecdf..7db3b045 100644 --- a/src/RNAseq.nf +++ b/src/RNAseq.nf @@ -304,7 +304,8 @@ fi } HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC; - HISAT_ALIGNED_DEDUP} + HISAT_ALIGNED_DEDUP; + HISAT_ALIGNED_COV} //////////////////////////// /* Fastqc of genome reads */ @@ -328,6 +329,27 @@ process fastqc_genome { """ } + +////////////// +/* Coverage */ +////////////// + +process coverage { + tag "$file_id" + publishDir "${params.output}/03_hisat2/coverage/", mode: 'copy' + + input: + set file_id, file(bam) from HISAT_ALIGNED_COV + + output: + file "*.bigwig" into COVERAGE_OUTPUT + + """ + bamCoverage -p ${task.cpus} --binSize 1 -b ${bam[0]} -o ${file_id}.bigwig + + """ +} + //////////////////////////// /* Deduplication of reads */ //////////////////////////// diff --git a/src/RibosomeProfiling.nf b/src/RibosomeProfiling.nf index 48ce6e55..7f572a23 100644 --- a/src/RibosomeProfiling.nf +++ b/src/RibosomeProfiling.nf @@ -291,7 +291,8 @@ fi } HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC; - HISAT_ALIGNED_DEDUP} + HISAT_ALIGNED_DEDUP; + HISAT_ALIGNED_COV} //////////////////////////// /* Fastqc of genome reads */ @@ -315,6 +316,25 @@ process fastqc_genome { """ } +////////////// +/* Coverage */ +////////////// + +process coverage { + tag "$file_id" + publishDir "${params.output}/03_hisat2/coverage/", mode: 'copy' + + input: + set file_id, file(bam) from HISAT_ALIGNED_COV + + output: + file "*.bigwig" into COVERAGE_OUTPUT + + """ + bamCoverage -p ${task.cpus} --binSize 1 -b ${bam[0]} -o ${file_id}.bigwig + """ +} + //////////////////////////// /* Deduplication of reads */ //////////////////////////// -- GitLab