diff --git a/main.nf b/main.nf
index fabc8746b5b122784fc44ad06190569f7d1e157e..65f2e1b5121b46e280fd94a2ed0d54c8039e48d1 100644
--- a/main.nf
+++ b/main.nf
@@ -1,6 +1,6 @@
nextflow.enable.dsl = 2
include {var_calling} from './pipeline/var_calling.nf'
-include {hello} from './pipeline/cnv_calling.nf'
+include {check_inputs} from './pipeline/cnv_calling.nf'
// which part of the pipeline to run - either 'variant-calling' or 'variant-prioritisation' or 'cnv-calling'
params.workflow = null
@@ -43,7 +43,7 @@ workflow {
println "Variant prioritisation coming soon"
} else if (params.workflow == 'cnv-calling') {
println "CNV identification pipeline in development"
- hello()
+ check_inputs()
} else {
exit 1, 'params.workflow required - variant-calling, cnv-calling or variant-prioritisation'
}
diff --git a/nextflow.config b/nextflow.config
index 585d5b2bf74d4c5b944474845291a0491c8b00fa..79bd9c5a66f09995bdb5b8bf66d9ada9d574bdd9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,4 +1,4 @@
-executor = 'slurm'
+// executor = 'slurm'
process {
@@ -18,7 +18,7 @@ process {
}
withLabel: large {
- cpus = 16
+ cpus = 10
memory = 32.GB
}
}
diff --git a/pipeline/cnv_calling.nf b/pipeline/cnv_calling.nf
index a93fd384992dc17277ce27138c5cf200c3b38346..7ca4cefd8b462d930373c22daf66378b77253a14 100644
--- a/pipeline/cnv_calling.nf
+++ b/pipeline/cnv_calling.nf
@@ -5,16 +5,97 @@ nextflow.enable.dsl = 2
include {read_inputs} from './inputs.nf'
include {validation} from './validation.nf'
-process HELLO {
+process check_argument_files {
+
+// a process to look at the files given as arguments and check they exist (ie provided in eddie.config)
+// as defaults are set to Null there may not be a 'problem' if one of these files is not found
+// arguments to be checked are: params.bcbio, params.bcbio_template, params.target_bed, params.reference_genome
+// params.parse_peddy_output
+// sample sheet and ped file are checked seperately
+ script:
+
+ """
+ echo "hello world"
+ """
+
+}
+
+
+process check_sample_sheet {
+ input:
+ val sample_sheet
+
script:
- "echo \"hello world\""
+
+ """
+ touch "$workflow.projectDir"/sample_sheet_check.txt
+
+ # echo $workflow.projectDir
+ # count the number of words in the first line of the sample sheet
+ # this is the number of columns. it is expected ther will be 3
+ # sample reads_1 reads_2
+
+ columns=\$(head -n 1 $sample_sheet| wc -w)
+
+ if( "\${columns}" != 3 ); then
+
+ echo "ERROR: $sample_sheet has an unexpected format" >> "$workflow.projectDir"/sample_sheet_check.txt
+
+ else
+
+ echo "$sample_sheet has expected number of columns" >> "$workflow.projectDir"/sample_sheet_check.txt
+
+
+ fi
+
+ # Then take columns 2 and 3, check that all fastqs listed exist
+ # use tail to ignore the header
+
+ reads_1=\$(cat $sample_sheet | cut -f2,3 | tail -n +2)
+
+ #check that the file exists
+
+ for file in \${reads_1};
+ do
+ # build up path to specified file
+
+ path_to_file=$workflow.projectDir
+ path_to_file+="/"
+ path_to_file+=\${file}
+
+ # check if they exist
+
+ if [ -f "\${path_to_file}" ]; then
+
+ echo "\"\${path_to_file}\" exist" >> "$workflow.projectDir"/sample_sheet_check.txt
+
+ else
+
+ # if file doesn't exist, should return error and exit
+
+ echo "\"\${path_to_file}\" does not exist" >> "$workflow.projectDir"/sample_sheet_check.txt
+ fi
+ done
+ """
}
+process check_ped_file {
+ input:
+ val ped_file
+
+ script:
+
+ """
+ cat $ped_file
+ """
+}
-workflow hello {
- HELLO()
+workflow check_inputs {
+ read_inputs()
+ check_sample_sheet(read_inputs.out.ch_samplesheet)
+ check_ped_file(read_inputs.out.ch_ped_file)
}
diff --git a/tests/assets/input_data/ped_files/giab_test_trios.ped b/tests/assets/input_data/ped_files/giab_test_trios.ped
index 566cce43692ccc031da29f5336c4a7130d093c25..3f3c4cd1905f2d8c0977695a90351906591b0692 100644
--- a/tests/assets/input_data/ped_files/giab_test_trios.ped
+++ b/tests/assets/input_data/ped_files/giab_test_trios.ped
@@ -1,6 +1,6 @@
00001_000001 000001_000001 000002_000002 000003_000002 1 2
00001_000001 000002_000001 0 0 1 1
00001_000001 000003_000001 0 0 2 1
-00001_000002 000004_000002 000005_000002 000006_000002 1 2
-00001_000002 000005_000002 0 0 1 1
-00001_000002 000006_000002 0 0 2 1
+# 00001_000002 000004_000002 000005_000002 000006_000002 1 2
+# 00001_000002 000005_000002 0 0 1 1
+# 00001_000002 000006_000002 0 0 2 1
diff --git a/tests/assets/input_data/sample_sheets/giab_test_non_trios.tsv b/tests/assets/input_data/sample_sheets/giab_test_non_trios.tsv
index cf341e536ed8bc95cb4856bf622b54cf44bceb4c..9ffd458c56fec4ac842e06c090b385aae026622e 100644
--- a/tests/assets/input_data/sample_sheets/giab_test_non_trios.tsv
+++ b/tests/assets/input_data/sample_sheets/giab_test_non_trios.tsv
@@ -1,8 +1,8 @@
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
-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_000003 assets/input_data/giab/AshkenazimTrio/HG002_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG002_R2.fastq.gz
-000006_000003 assets/input_data/giab/ChineseTrio/HG005_R1.fastq.gz assets/input_data/giab/ChineseTrio/HG005_R2.fastq.gz
-000007_000003 assets/input_data/giab/AshkenazimTrio/HG003_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG003_R2.fastq.gz
-000008_000003 assets/input_data/giab/AshkenazimTrio/HG004_R1.fastq.gz assets/input_data/giab/AshkenazimTrio/HG004_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
+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_000003 assets/input_data/scripts/giab/AshkenazimTrio/HG002_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG002_R2.fastq.gz
+000006_000003 assets/input_data/scripts/giab/ChineseTrio/HG005_R1.fastq.gz assets/input_data/scripts/giab/ChineseTrio/HG005_R2.fastq.gz
+000007_000003 assets/input_data/scripts/giab/AshkenazimTrio/HG003_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG003_R2.fastq.gz
+000008_000003 assets/input_data/scripts/giab/AshkenazimTrio/HG004_R1.fastq.gz assets/input_data/scripts/giab/AshkenazimTrio/HG004_R2.fastq.gz
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 f7b152609625ee8cc5c6a8e5f7cc92376d57b894..0a45838d53b59b68d8a3520e2c392a34d5ad6a3d 100644
--- a/tests/assets/input_data/sample_sheets/giab_test_trios.tsv
+++ b/tests/assets/input_data/sample_sheets/giab_test_trios.tsv
@@ -2,6 +2,7 @@ individual_id read_1 read_2
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
+# 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/sample_sheets/giab_test_trios.tsv.save b/tests/assets/input_data/sample_sheets/giab_test_trios.tsv.save
new file mode 100644
index 0000000000000000000000000000000000000000..5f0269375b4ba1480855f4507f46328a1f064988
--- /dev/null
+++ b/tests/assets/input_data/sample_sheets/giab_test_trios.tsv.save
@@ -0,0 +1,6 @@
+individual_id read_1 read_2
+0f00001_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
+00003_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
diff --git a/tests/run_giab_tests.sh b/tests/run_giab_tests.sh
index 1a685561200b538e9e6b85bdfa5efe98f7d32dfc..3b965562743edb755162b0e643a20c77dc34b65d 100644
--- a/tests/run_giab_tests.sh
+++ b/tests/run_giab_tests.sh
@@ -3,7 +3,7 @@
source scripts/nextflow_detached.sh
test_exit_status=0
-nextflow -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config clean -f
+# nextflow -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config clean -f
echo "Reduced GiaB data - trios"
run_nextflow ../main.nf \
@@ -16,14 +16,14 @@ run_nextflow ../main.nf \
test_exit_status=$(( $test_exit_status + $? ))
-echo "Reduced GiaB data - non-trios"
-run_nextflow ../main.nf \
- -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config \
- --workflow "variant-calling" \
- --pipeline_project_id giab_test_non_trios \
- --pipeline_project_version v1 \
- --ped_file $PWD/assets/input_data/ped_files/giab_test_non_trios.ped \
- --sample_sheet $PWD/assets/input_data/sample_sheets/giab_test_non_trios.tsv
+#echo "Reduced GiaB data - non-trios"
+#run_nextflow ../main.nf \
+# -c /exports/igmm/eddie/IGMM-VariantAnalysis/emma/eddie.config \
+# --workflow "variant-calling" \
+# --pipeline_project_id giab_test_non_trios \
+# --pipeline_project_version v1 \
+# --ped_file $PWD/assets/input_data/ped_files/giab_test_non_trios.ped \
+# --sample_sheet $PWD/assets/input_data/sample_sheets/giab_test_non_trios.tsv
test_exit_status=$(( $test_exit_status + $? ))
diff --git a/tests/scripts/bcbio_nextgen.py b/tests/scripts/bcbio_nextgen.py
old mode 100755
new mode 100644
diff --git a/tests/scripts/bcbio_prepare_samples.py b/tests/scripts/bcbio_prepare_samples.py
old mode 100755
new mode 100644