From 5f215dd440f8fff1ad083d4cc9ca36fb910b9853 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Mar 2023 13:55:56 +0200
Subject: [PATCH] add nextflow pipeline for fastkmers
---
data/sample.csv | 14 ++++++++++++++
src/main.nf | 22 ++++++++++++++++++++++
src/modules/fastkmers.nf | 28 ++++++++++++++++++++++++++++
src/nextflow.config | 39 +++++++++++++++++++++++++++++++++++++++
4 files changed, 103 insertions(+)
create mode 100644 data/sample.csv
create mode 100644 src/main.nf
create mode 100644 src/modules/fastkmers.nf
create mode 100644 src/nextflow.config
diff --git a/data/sample.csv b/data/sample.csv
new file mode 100644
index 0000000..091534e
--- /dev/null
+++ b/data/sample.csv
@@ -0,0 +1,14 @@
+specie; sex; r1; r2
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fasta.gz
+mbelari; female; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fasta.gz
+mbelari; male; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fasta.gz
+mbelari; male; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fasta.gz
+mlongespiculosa; female; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fasta.gz
+mlongespiculosa; male; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz
+mspiculigera; female; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fasta.gz
+mspiculigera; male; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fasta.gz
diff --git a/src/main.nf b/src/main.nf
new file mode 100644
index 0000000..a0194eb
--- /dev/null
+++ b/src/main.nf
@@ -0,0 +1,22 @@
+nextflow.enable.dsl=2
+
+/*
+Testing pipeline for marseq scRNASeq analysis
+*/
+
+include { FASTKMERS } from "./modules/fastkmers.nf"
+
+
+Channel.fromPath( file(params.csv) )
+ .splitCsv(header: true)
+ .map{row ->
+ fastq_r1 = file("${r1}")
+ fastq_r2 = file("${r2}")
+ meta = ['id': ${fastq_r1.simpleName},, 'specie': ${specie}, 'sex': ${sex}]
+ [meta, [fastq_r1, fastq_r2]]
+ }
+ .set{ fastq }
+
+workflow {
+ FASTLMERS(fastq)
+}
diff --git a/src/modules/fastkmers.nf b/src/modules/fastkmers.nf
new file mode 100644
index 0000000..5a77b0a
--- /dev/null
+++ b/src/modules/fastkmers.nf
@@ -0,0 +1,28 @@
+/*
+ * normalize bam file
+ */
+process FASTKMERS {
+ tag "$meta.id"
+ label 'process_single'
+
+ container "lbmc/fastkmers:025efdf"
+
+ input:
+ tuple val(meta), path(fastq)
+
+ output:
+ tuple val(meta), path("*.csv"), emit: csv
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ fastkmers -k 31 ${fastq} > ${fastq.simpleName}.csv
+
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ fastkmers: \$(echo \$(fastkmers --version 2>&1))
+ END_VERSIONS
+ """
+}
diff --git a/src/nextflow.config b/src/nextflow.config
new file mode 100644
index 0000000..6b90004
--- /dev/null
+++ b/src/nextflow.config
@@ -0,0 +1,39 @@
+psmn {
+ charliecloud.enabled = true
+ charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
+ charliecloud.readOnlyInputs = true
+ charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
+
+ process{
+ errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+ maxRetries = 3
+ executor = "slurm"
+ queue = "Lake"
+ withLabel: big_mem_mono_cpus {
+ cpus = 1
+ memory = "128GB"
+ time = "24h"
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 32
+ memory = "192GB"
+ time = "24h"
+ }
+ withLabel: small_mem_mono_cpus {
+ cpus = 1
+ memory = "16GB"
+ time = "24h"
+ }
+ withLabel: small_mem_multi_cpus {
+ cpus = 32
+ memory = "16GB"
+ time = "24h"
+ }
+ }
+
+ params {
+ max_memory = 512.GB
+ max_cpus = 32
+ max_time = 24.h
+ }
+}
--
GitLab