Skip to content
Snippets Groups Projects
Commit acd6068e authored by mwham's avatar mwham
Browse files

Making min/max resources configurable, adding test stubs

parent abf8d102
No related branches found
No related tags found
2 merge requests!10Merge in master,!8Bin dir, CI build fixes
Pipeline #14806 failed
Showing
with 59 additions and 53 deletions
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.gz
ff8e9778919b20dd68feb85d98dd71c1 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.gz
c29c49cb98fa142d55f15593db614bb1 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.gz
a8be92b4125079047231d908878b629b 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.gz
fdfff34f486e4983ed7fcfb01a27b94b 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.gz
5ce6fd40ff99de36cc1349b10ed4e84d 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.gz
a61eaa2e396dd876331cbc7d80e0a97e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.gz
cc18d33f52a274ca942e5ab6658eb2ea 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.gz
e194ff7dd2f6ccccb91924fe4ec5e42f 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.gz
df1a24a8a06148c630bc28e13e781afd 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.gz
698fe14b092b458d55999bb93e03e5b7 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.gz
57ca2fbf2e23d090db7b259263ab7745 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.gz
b5b39a73e5a795f95ec619d392beb396 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.gz
21b06127503d2ab8b177d68c9a91721d 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.gz
4392717bb3aa768a9eb0c04aef9c69bc 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.gz
9583a802f8adfe12b7231475af7ee0bd 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.count
d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.gz
70cb93d77d74cd2c891987151a92f38a 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_1.fastq.count
dc9b03bd11623d4849c51f2ca048a4fc 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_2.fastq.count
df6f6f0def68997002213e94fedbe4c5 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_2.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_1.fastq.count
7ca1184e141e53014a8330aca0674315 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_1.fastq.gz
d41d8cd98f00b204e9800998ecf8427e 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.count
d7f2cafffa026c278b79faf113fc79e9 12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.gz
#!/bin/bash
source scripts/nextflow_detached.sh
bcbio=$PWD/scripts/bcbio_nextgen.py
test_exit_status=0
rm -r work/*/*
echo "Test case 1: simple trio"
run_nextflow ../main.nf \
-stub-run -profile stubs \
--workflow variant-calling \
--pipeline_project_id test_stub \
--pipeline_project_version v1 \
--ped_file assets/input_data/ped_files/batch_1.ped \
--sample_sheet assets/input_data/sample_sheets/batch_1.tsv
test_exit_status=$(( $test_exit_status + $? ))
echo "Test case 2: MD5 errors"
run_nextflow ../main.nf \
-stub-run -profile stubs \
--workflow variant-calling \
--pipeline_project_id test_stub_md5_errors \
--pipeline_project_version v1 \
--ped_file assets/input_data/ped_files/batch_2_md5_errors.ped \
--sample_sheet assets/input_data/sample_sheets/batch_2_md5_errors.tsv
if [ $? == 0 ]
then
test_exit_status=$(( $test_exit_status + 1 ))
fi
echo "Tests finished with exit status $test_exit_status"
#!/bin/bash
source scripts/nextflow_detached.sh
bcbio=$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/bcbio/bcbio_template.yaml"
test_exit_status=0
nextflow clean -f
echo "Test case 1: simple trio"
run_nextflow ../pipeline/main.nf --ped_file assets/input_data/ped_files/batch_1.ped --sample_sheet assets/input_data/sample_sheets/batch_1.tsv $common_args
test_exit_status=$(( $test_exit_status + $? ))
for f in "
outputs/individuals/000001/merged_fastqs/000001_merged_r1.fastq.gz
outputs/individuals/000001/merged_fastqs/000001_merged_r2.fastq.gz
outputs/individuals/000002/merged_fastqs/000002_merged_r1.fastq.gz
outputs/individuals/000002/merged_fastqs/000002_merged_r2.fastq.gz
outputs/individuals/000003/merged_fastqs/000003_merged_r1.fastq.gz
outputs/individuals/000003/merged_fastqs/000003_merged_r2.fastq.gz
outputs/families/000001/000001.csv
"
do
ls $f > /dev/null
test_exit_status=$(( $test_exit_status + $? ))
done
echo "Test case 2: MD5 errors"
run_nextflow ../pipeline/main.nf --ped_file assets/input_data/ped_files/batch_2_md5_errors.ped --sample_sheet assets/input_data/sample_sheets/batch_2_md5_errors.tsv $common_args
if [ $? == 0 ]
then
test_exit_status=$(( $test_exit_status + 1 ))
fi
echo "Tests finished with exit status $test_exit_status"
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment