correct nextflow.config

nextflow.config

+executor = 'slurm'
 
 process {
-    executor = 'slurm'
+
     cpus = 4
     memory = 8.GB
     time = '6h'

tests/assets/input_data/sample_sheets/giab_test_trios.tsv

 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

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

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 \