From 372438eee97aa26614455436e680e2f91146dd4f Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Thu, 17 Aug 2023 17:55:12 +0200
Subject: [PATCH] Add Alignment Score filtration but need to take into account
the length of reads.
---
.../samtools/1.14/docker_init.sh | 8 +++---
src/.docker_modules/samtools/1.17/Dockerfile | 1 +
.../samtools/1.17/docker_init.sh | 5 ++++
src/bolero.nf | 12 ++++++---
src/nextflow.config | 2 +-
src/nf_modules/porechop/main.nf | 6 +++--
src/nf_modules/samtools/main.nf | 27 +++++++++++++++++--
7 files changed, 48 insertions(+), 13 deletions(-)
create mode 100644 src/.docker_modules/samtools/1.17/Dockerfile
create mode 100755 src/.docker_modules/samtools/1.17/docker_init.sh
diff --git a/src/.docker_modules/samtools/1.14/docker_init.sh b/src/.docker_modules/samtools/1.14/docker_init.sh
index 1d4a215..d76951f 100755
--- a/src/.docker_modules/samtools/1.14/docker_init.sh
+++ b/src/.docker_modules/samtools/1.14/docker_init.sh
@@ -1,5 +1,5 @@
#!/bin/sh
-docker pull lbmc/samtools:1.14
-# docker build src/.docker_modules/samtools/1.14 -t 'lbmc/samtools:1.14'
-# docker push lbmc/samtools:1.14
-docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samtools:1.14" --push src/.docker_modules/samtools/1.14
+# docker pull xgrand/samtools:1.14
+docker build src/.docker_modules/samtools/1.14 -t 'xgrand/samtools:1.14'
+docker push xgrand/samtools:1.14
+# docker buildx build --platform linux/amd64,linux/arm64 -t "xgrand/samtools:1.14" --push src/.docker_modules/samtools/1.14
diff --git a/src/.docker_modules/samtools/1.17/Dockerfile b/src/.docker_modules/samtools/1.17/Dockerfile
new file mode 100644
index 0000000..b7d7973
--- /dev/null
+++ b/src/.docker_modules/samtools/1.17/Dockerfile
@@ -0,0 +1 @@
+FROM staphb/samtools:1.17-2023-06
\ No newline at end of file
diff --git a/src/.docker_modules/samtools/1.17/docker_init.sh b/src/.docker_modules/samtools/1.17/docker_init.sh
new file mode 100755
index 0000000..df2e0b6
--- /dev/null
+++ b/src/.docker_modules/samtools/1.17/docker_init.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+# docker pull xgrand/samtools:1.17
+docker build src/.docker_modules/samtools/1.17 -t 'xgrand/samtools:1.17'
+docker push xgrand/samtools:1.17
+# docker buildx build --platform linux/amd64,linux/arm64 -t "xgrand/samtools:1.17" --push src/.docker_modules/samtools/1.17
diff --git a/src/bolero.nf b/src/bolero.nf
index 159be2a..2bb2162 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -104,10 +104,11 @@ params.kit_barcoding = ""
params.basecalling_out = "01_basecalling/"
params.barcoding_out = "02_barcoding/"
params.fastq_out = "03_fastq/"
-params.seqkit_grep_out = "14_seqkit/"
-params.porechop_out = "15_porechop/"
+params.seqkit_grep_out = "03_fastq/"
+params.porechop_out = "03_fastq/"
params.cutadapt_out = "04_cutadapt/"
params.minimap2_genome_out = "05_minimap2/"
+params.filtered_bam_out = "05_minimap2/"
params.start_position_counts_out = "06_start_positions/"
params.nanosplicer_out = "07_nanosplicer/"
params.rna_count_out = "08_RNA_count/"
@@ -171,7 +172,6 @@ if(!params.skipBC) {
}
}
-// include { barecode } from "./nf_modules/barecode/main.nf"
include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
include { control_bam } from "./nf_modules/pycoqc/main.nf"
@@ -182,6 +182,7 @@ include { seqkit_grep } from "./nf_modules/seqkit/main.nf"
include { sort_bam } from './nf_modules/samtools/main.nf' addParams(sort_bam_out: params.minimap2_genome_out)
include { index_bam } from './nf_modules/samtools/main.nf' addParams(index_bam_out: params.minimap2_genome_out)
include { sort_index_bam } from './nf_modules/samtools/main.nf' addParams(indexed_bam_out: params.minimap2_genome_out)
+include { filter_as } from './nf_modules/samtools/main.nf'
include { start_position_counts } from "./nf_modules/samtools/main.nf"
include { start_position_individuals } from "./nf_modules/start_positions/main.nf"
include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
@@ -258,8 +259,11 @@ workflow {
hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
+ //Filter
+ filter_as(hbv_genome.out.bam)
+
//Index
- sort_index_bam(hbv_genome.out.bam)
+ sort_index_bam(filter_as.out.filtered_bam)
//Quality control
if(params.skipBC == false) {
diff --git a/src/nextflow.config b/src/nextflow.config
index 4b6a530..b087fb3 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -18,7 +18,7 @@ profiles {
docker.enabled = true
process {
errorStrategy = 'finish'
- memory = '12GB'
+ memory = '16GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
diff --git a/src/nf_modules/porechop/main.nf b/src/nf_modules/porechop/main.nf
index 8f69462..8513104 100755
--- a/src/nf_modules/porechop/main.nf
+++ b/src/nf_modules/porechop/main.nf
@@ -4,7 +4,7 @@ container_url = "xgrand/porechop:${version}"
params.porechop_out = ""
process porechop {
container = "${container_url}"
- label "small_mem_multi_cpus"
+ label "big_mem_multi_cpus"
tag "$barcode"
if (params.porechop_out != "") {
publishDir "results/${params.porechop_out}", mode: 'copy'
@@ -14,9 +14,11 @@ process porechop {
tuple val(barcode), path(fastq)
output:
- tuple val(barcode), path("*"), emit: porechoped_fastq
+ tuple val(barcode), path("${barcode}/${barcode}_merged_porechoped.fastq.gz"), emit: porechoped_fastq
script:
"""
+mkdir ${barcode}
+cd ${barcode}/
porechop --input ${fastq} -o ${barcode}_merged_porechoped.fastq.gz --threads ${task.cpus}
"""
}
\ No newline at end of file
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 854c4f1..eae5423 100755
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -1,5 +1,5 @@
-version = "1.7"
-container_url = "lbmc/samtools:${version}"
+version = "1.17"
+container_url = "xgrand/samtools:${version}"
params.sort_bam_out =""
process sort_bam {
@@ -87,4 +87,27 @@ cd ${barcode}/
samtools sort -@ ${task.cpus} ../${bam} -o ${barcode}_sorted.bam
samtools index -@ ${task.cpus} ${barcode}_sorted.bam
"""
+}
+
+params.filtered_bam_out = ""
+process filter_as {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "${barcode}"
+ if (params.filtered_bam_out != "") {
+ publishDir "results/${params.filtered_bam_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(barcode), path(bam)
+
+ output:
+ tuple val(barcode), path("${barcode}/*_AS500.bam"), emit: filtered_bam
+
+ script:
+"""
+mkdir ${barcode}
+cd ${barcode}/
+samtools view -Shb -e '[AS]>=500' -@ ${task.cpus} ../${bam} -o ${barcode}_AS500.bam
+"""
}
\ No newline at end of file
--
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