From 607d6f79ff78c716e7fe05f9fe0017736554b5a9 Mon Sep 17 00:00:00 2001
From: 3mma-mack <emzmackenz13@gmail.com>
Date: Mon, 23 May 2022 10:12:39 +0100
Subject: [PATCH] correct nextflow.config
---
nextflow.config | 3 ++-
.../input_data/sample_sheets/giab_test_trios.tsv | 12 ++++++------
tests/assets/input_data/scripts/giab.sh | 8 ++++----
tests/run_giab_tests.sh | 12 +++---------
4 files changed, 15 insertions(+), 20 deletions(-)
mode change 100755 => 100644 tests/assets/input_data/scripts/giab.sh
diff --git a/nextflow.config b/nextflow.config
index d861ce3..585d5b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,7 @@
+executor = 'slurm'
process {
- executor = 'slurm'
+
cpus = 4
memory = 8.GB
time = '6h'
diff --git a/tests/assets/input_data/sample_sheets/giab_test_trios.tsv b/tests/assets/input_data/sample_sheets/giab_test_trios.tsv
index 35429e7..f7b1526 100644
--- a/tests/assets/input_data/sample_sheets/giab_test_trios.tsv
+++ b/tests/assets/input_data/sample_sheets/giab_test_trios.tsv
@@ -1,7 +1,7 @@
individual_id read_1 read_2
-000001_000001 assets/input_data/giab/AshkenazimTrio/HG002_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG002_R2.fastq.gz
-000002_000001 assets/input_data/giab/AshkenazimTrio/HG003_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG003_R2.fastq.gz
-000003_000001 assets/input_data/giab/AshkenazimTrio/HG004_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG004_R2.fastq.gz
-000004_000002 assets/input_data/giab/ChineseTrio/HG005_R1.fastq.gz assets/input_data/giab/ChineseTrio/HG005_R2.fastq.gz
-000005_000002 assets/input_data/giab/ChineseTrio/HG006_R1.fastq.gz assets/input_data/giab/ChineseTrio/HG006_R2.fastq.gz
-000006_000002 assets/input_data/giab/ChineseTrio/HG007_R1.fastq.gz assets/input_data/giab/ChineseTrio/HG007_R2.fastq.gz
+000001_000001 assets/input_data/scripts/giab/AshkenazimTrio/HG002_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG002_R2.fastq.gz
+000002_000001 assets/input_data/scripts/giab/AshkenazimTrio/HG003_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG003_R2.fastq.gz
+000003_000001 assets/input_data/scripts/giab/AshkenazimTrio/HG004_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG004_R2.fastq.gz
+000004_000002 assets/input_data/scripts/giab/ChineseTrio/HG005_R1.fastq.gz assets/input_data/scripts/giab/ChineseTrio/HG005_R2.fastq.gz
+000005_000002 assets/input_data/scripts/giab/ChineseTrio/HG006_R1.fastq.gz assets/input_data/scripts/giab/ChineseTrio/HG006_R2.fastq.gz
+000006_000002 assets/input_data/scripts/giab/ChineseTrio/HG007_R1.fastq.gz assets/input_data/scripts/giab/ChineseTrio/HG007_R2.fastq.gz
diff --git a/tests/assets/input_data/scripts/giab.sh b/tests/assets/input_data/scripts/giab.sh
old mode 100755
new mode 100644
index 3a8b9fb..91d4dc4
--- a/tests/assets/input_data/scripts/giab.sh
+++ b/tests/assets/input_data/scripts/giab.sh
@@ -8,7 +8,7 @@
# bedtools
# bazam
-TWIST_TARGET=Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+TWIST_TARGET="../Twist_Exome_RefSeq_targets_hg38.plus15bp.bed"
###
# Prepare the chr22 target subset
@@ -47,7 +47,7 @@ do
samtools index $bam_base
# Extract FASTQ
- java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+ java -jar ../../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
# Gzip the FASTQ reads
gzip *.fastq
@@ -90,7 +90,7 @@ do
samtools index $bam_base
# Extract FASTQ
- java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+ java -jar ../../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
# Gzip the FASTQ reads
gzip *.fastq
@@ -135,7 +135,7 @@ do
samtools index $bam_base
# Extract FASTQ
- java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+ java -jar ../../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
# Gzip the FASTQ reads
gzip *.fastq
diff --git a/tests/run_giab_tests.sh b/tests/run_giab_tests.sh
index 66f6df2..1a68556 100644
--- a/tests/run_giab_tests.sh
+++ b/tests/run_giab_tests.sh
@@ -2,29 +2,23 @@
source scripts/nextflow_detached.sh
-bcbio=$PWD/scripts/bcbio_nextgen.py
-bcbio_prepare_samples=$PWD/scripts/bcbio_prepare_samples.py
-
-common_args="--bcbio $bcbio --bcbio_prepare_samples $bcbio_prepare_samples --bcbio_template $PWD/scripts/trio_whole_exome_bcbio_template.yaml"
-
test_exit_status=0
-nextflow -c "$NEXTFLOW_CONFIG" clean -f
+nextflow -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config clean -f
echo "Reduced GiaB data - trios"
run_nextflow ../main.nf \
- -c "$NEXTFLOW_CONFIG" \
+ -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config \
--workflow "variant-calling" \
--pipeline_project_id giab_test_trios \
--pipeline_project_version v1 \
--ped_file $PWD/assets/input_data/ped_files/giab_test_trios.ped \
--sample_sheet $PWD/assets/input_data/sample_sheets/giab_test_trios.tsv \
- $common_args
test_exit_status=$(( $test_exit_status + $? ))
echo "Reduced GiaB data - non-trios"
run_nextflow ../main.nf \
- -c "$NEXTFLOW_CONFIG" \
+ -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config \
--workflow "variant-calling" \
--pipeline_project_id giab_test_non_trios \
--pipeline_project_version v1 \
--
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