Making min/max resources configurable, adding test stubs

tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/md5sums.txt

 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

tests/run_stubs.sh

+#!/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"

tests/run_tests.sh

-#!/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"