From 9131c8e07e5ec1da81b27f7c855336127267a59a Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 1 Oct 2020 17:19:55 -0500
Subject: [PATCH] update with singularity
---
nextflow.config | 21 ++++++++++++---------
workflow/main.nf | 10 +++-------
workflow/process_scripts | 2 +-
3 files changed, 16 insertions(+), 17 deletions(-)
diff --git a/nextflow.config b/nextflow.config
index a153714..b187420 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,22 +6,25 @@ process {
clusterOptions = '--hold --no-kill'
queue = '128GB,256GB,256GBv1'
withLabel: trim {
- container = 'goalconsortium/trim_galore:1.0.4'
+ container = 'trim_galore.sif'
}
withLabel: dnaalign {
- container = 'goalconsortium/dna_alignment:1.0.4'
+ container = 'dna_alignment.sif'
}
withLabel: profiling_qc {
- container = 'goalconsortium/profiling_qc:1.0.4'
+ container = 'profiling_qc.sif'
}
- withName: starfusion {
- container = 'goalconsortium/starfusion:1.0.4'
+ withLabel: starfusion {
+ container = 'starfusion.sif'
}
- withName: ralign {
- container = 'goalconsortium/rna_alignment:1.0.4'
+ withLabel: ralign {
+ container = 'rna_alignment.sif'
}
- withName: geneabund {
- container = 'goalconsortium/rna_gene_abundance:1.0.4'
+ withLabel: geneabund {
+ container = 'rna_gene_abundance.sif'
+ }
+ withLabel: rnaseqstat {
+ container = 'rnaseq_dea.sif'
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index 1f45983..ea17a58 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -34,23 +34,18 @@ index_path = file(params.genome)
process checkdesignfile {
queue 'super'
- module 'parallel/20150122:pigz/2.4'
+ label 'trim'
publishDir "$params.output", mode: 'copy'
-
input:
file design_file name 'design.ori.txt'
file ("*") from fqs.collect()
-
output:
file("design.valid.txt") into newdesign
file("*.fastq.gz") into fastqs mode flatten
stdout spltnames
-
script:
"""
- bash $baseDir/scripts/check_inputfiles.sh
- perl -p -e 's/\\r\\n*/\\n/g' design.ori.txt > design.fix.txt
- perl $baseDir/scripts/check_designfile.pl ${params.pairs} design.fix.txt
+ bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
"""
}
@@ -159,6 +154,7 @@ process geneabund {
process statanal {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
+ label 'rnaseqstat'
input:
file count_file from counts.toList()
file count_sum from ctsum.toList()
diff --git a/workflow/process_scripts b/workflow/process_scripts
index 96bcf78..8706de7 160000
--- a/workflow/process_scripts
+++ b/workflow/process_scripts
@@ -1 +1 @@
-Subproject commit 96bcf78802267e8bb1834c06ffb98c5d700273e3
+Subproject commit 8706de703b8b5933f89651e5be0312af96cddb7c
--
GitLab